MiMeDB: Showing metabocard for IDP (MMDBc0032840)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 22:01:47 UTC

Update Date

2024-04-30 19:54:39 UTC

Metabolite ID

MMDBc0032840

Metabolite Identification

Common Name

IDP

Description

IDP is an inosine nucleotide containing a pyrophosphate group esterified to the C5 of the sugar moiety.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv0541 02231219412D          

 27 29  0  0  1  0            999 V2000
   26.6615  -10.0907    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   26.9610   -8.6935    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   26.4078   -9.3057    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.9151  -10.8757    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.4465   -9.8371    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.5141   -8.0814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.3489   -8.1404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.0649  -13.8404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.0680  -12.0455    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.1294  -12.9396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.8764  -10.3443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.5731   -9.2466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.8618  -16.7060    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.3569  -14.3921    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.8618  -14.2310    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.1473  -15.4685    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.3569  -15.7199    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.3620  -11.4879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.6132  -13.6078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.6155  -12.2730    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   27.3983  -13.3543    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   27.3998  -12.5293    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   25.5763  -14.6435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.8618  -15.8810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5763  -15.4685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.1473  -14.6435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.8384  -15.0560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  1 11  2  0  0  0  0
  2  3  1  0  0  0  0
  2  6  1  0  0  0  0
  2  7  1  0  0  0  0
  2 12  2  0  0  0  0
  4 18  1  0  0  0  0
 21  8  1  1  0  0  0
 22  9  1  1  0  0  0
 10 19  1  0  0  0  0
 10 20  1  0  0  0  0
 13 24  2  0  0  0  0
 14 19  1  0  0  0  0
 14 23  1  0  0  0  0
 14 27  1  0  0  0  0
 15 23  1  0  0  0  0
 15 26  1  0  0  0  0
 16 24  1  0  0  0  0
 16 26  2  0  0  0  0
 17 25  1  0  0  0  0
 17 27  2  0  0  0  0
 20 18  1  6  0  0  0
 19 21  1  0  0  0  0
 20 22  1  0  0  0  0
 21 22  1  0  0  0  0
 23 25  2  0  0  0  0
 24 25  1  0  0  0  0
M  END

HMDB0003335
     RDKit          3D
IDP
 41 43  0  0  0  0  0  0  0  0999 V2000
   -7.0368    1.4313   -0.7051 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9814    0.8010   -0.9499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8881    0.1500   -2.1193 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7598   -0.5427   -2.4176 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7534   -0.5605   -1.5266 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7984    0.0752   -0.3421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9316    0.7730   -0.0386 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7691    1.3253    1.1759 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5461    0.9609    1.5978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9338    0.2046    0.7023 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6443   -0.4309    0.6632 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8864    0.1591   -0.3172 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2565    0.6675    0.2285 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4642   -0.2087   -0.0258 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6171    0.3318    0.5405 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9673   -0.6267    0.2690 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.7825   -1.9257    1.0276 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2952    0.1593    0.9944 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2497   -0.9036   -1.3738 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4509    0.1723   -1.8813 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.8082    1.5600   -1.9187 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0621   -0.2482   -3.4081 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6577    0.2109   -0.7091 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0615    0.7309    1.7318 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4976    1.9515    2.0297 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8776   -0.4360    1.9113 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5681   -0.4360    3.0837 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7356   -1.0487   -3.3710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9077   -1.1026   -1.7940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0988    1.2380    2.5436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8288   -1.4919    0.3463 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4577    1.6952   -0.1866 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6210   -0.4007   -1.1048 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2834   -1.1720    0.5142 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1464    1.1379    0.8170 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0330   -0.4052   -3.2839 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4827   -0.2206   -1.0957 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0249    0.5719    2.2644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7149    2.4920    1.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2152   -1.3522    1.9139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3484   -1.0143    3.0031 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 20 23  1  0
 13 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  1  0
  7  2  1  0
 26 11  1  0
 10  6  1  0
  4 28  1  0
  5 29  1  0
  9 30  1  0
 11 31  1  0
 13 32  1  6
 14 33  1  0
 14 34  1  0
 18 35  1  0
 22 36  1  0
 23 37  1  0
 24 38  1  1
 25 39  1  0
 26 40  1  6
 27 41  1  0
M  END


  Mrv0541 02231219412D          

 27 29  0  0  1  0            999 V2000
   26.6615  -10.0907    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   26.9610   -8.6935    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   26.4078   -9.3057    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.9151  -10.8757    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.4465   -9.8371    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.5141   -8.0814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.3489   -8.1404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.0649  -13.8404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.0680  -12.0455    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.1294  -12.9396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.8764  -10.3443    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.5731   -9.2466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.8618  -16.7060    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.3569  -14.3921    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.8618  -14.2310    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.1473  -15.4685    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.3569  -15.7199    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.3620  -11.4879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.6132  -13.6078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.6155  -12.2730    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   27.3983  -13.3543    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   27.3998  -12.5293    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   25.5763  -14.6435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.8618  -15.8810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5763  -15.4685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.1473  -14.6435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.8384  -15.0560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  1 11  2  0  0  0  0
  2  3  1  0  0  0  0
  2  6  1  0  0  0  0
  2  7  1  0  0  0  0
  2 12  2  0  0  0  0
  4 18  1  0  0  0  0
 21  8  1  1  0  0  0
 22  9  1  1  0  0  0
 10 19  1  0  0  0  0
 10 20  1  0  0  0  0
 13 24  2  0  0  0  0
 14 19  1  0  0  0  0
 14 23  1  0  0  0  0
 14 27  1  0  0  0  0
 15 23  1  0  0  0  0
 15 26  1  0  0  0  0
 16 24  1  0  0  0  0
 16 26  2  0  0  0  0
 17 25  1  0  0  0  0
 17 27  2  0  0  0  0
 20 18  1  6  0  0  0
 19 21  1  0  0  0  0
 20 22  1  0  0  0  0
 21 22  1  0  0  0  0
 23 25  2  0  0  0  0
 24 25  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032840

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@@H]1[C@@H](COP(O)(=O)OP(O)(O)=O)OC([C@@H]1O)N1C=NC2=C1NC=NC2=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N4O11P2/c15-6-4(1-23-27(21,22)25-26(18,19)20)24-10(7(6)16)14-3-13-5-8(14)11-2-12-9(5)17/h2-4,6-7,10,15-16H,1H2,(H,21,22)(H,11,12,17)(H2,18,19,20)/t4-,6-,7-,10?/m1/s1

> <INCHI_KEY>
JPXZQMKKFWMMGK-VTHZCTBJSA-N

> <FORMULA>
C10H14N4O11P2

> <MOLECULAR_WEIGHT>
428.1859

> <EXACT_MASS>
428.013430334

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
33.7480237727735

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[(2R,3S,4R)-3,4-dihydroxy-5-(6-oxo-6,9-dihydro-3H-purin-9-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <ALOGPS_LOGP>
-0.99

> <JCHEM_LOGP>
-3.588285764237081

> <ALOGPS_LOGS>
-2.00

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.3209774826690954

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.654971809008338

> <JCHEM_PKA_STRONGEST_BASIC>
1.7269501042007134

> <JCHEM_POLAR_SURFACE_AREA>
222.26

> <JCHEM_REFRACTIVITY>
82.6442

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.26e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{[(2R,3S,4R)-3,4-dihydroxy-5-(6-oxo-3H-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0003335
     RDKit          3D
IDP
 41 43  0  0  0  0  0  0  0  0999 V2000
   -7.0368    1.4313   -0.7051 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9814    0.8010   -0.9499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8881    0.1500   -2.1193 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7598   -0.5427   -2.4176 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7534   -0.5605   -1.5266 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7984    0.0752   -0.3421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9316    0.7730   -0.0386 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7691    1.3253    1.1759 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5461    0.9609    1.5978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9338    0.2046    0.7023 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6443   -0.4309    0.6632 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8864    0.1591   -0.3172 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2565    0.6675    0.2285 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4642   -0.2087   -0.0258 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6171    0.3318    0.5405 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9673   -0.6267    0.2690 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.7825   -1.9257    1.0276 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2952    0.1593    0.9944 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2497   -0.9036   -1.3738 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4509    0.1723   -1.8813 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.8082    1.5600   -1.9187 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0621   -0.2482   -3.4081 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6577    0.2109   -0.7091 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0615    0.7309    1.7318 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4976    1.9515    2.0297 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8776   -0.4360    1.9113 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5681   -0.4360    3.0837 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7356   -1.0487   -3.3710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9077   -1.1026   -1.7940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0988    1.2380    2.5436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8288   -1.4919    0.3463 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4577    1.6952   -0.1866 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6210   -0.4007   -1.1048 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2834   -1.1720    0.5142 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1464    1.1379    0.8170 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0330   -0.4052   -3.2839 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4827   -0.2206   -1.0957 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0249    0.5719    2.2644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7149    2.4920    1.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2152   -1.3522    1.9139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3484   -1.0143    3.0031 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 20 23  1  0
 13 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  1  0
  7  2  1  0
 26 11  1  0
 10  6  1  0
  4 28  1  0
  5 29  1  0
  9 30  1  0
 11 31  1  0
 13 32  1  6
 14 33  1  0
 14 34  1  0
 18 35  1  0
 22 36  1  0
 23 37  1  0
 24 38  1  1
 25 39  1  0
 26 40  1  6
 27 41  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  P   UNK     0      49.768 -18.836   0.000  0.00  0.00           P+0
HETATM    2  P   UNK     0      50.327 -16.228   0.000  0.00  0.00           P+0
HETATM    3  O   UNK     0      49.295 -17.371   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      50.242 -20.301   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      51.233 -18.363   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      51.360 -15.085   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      49.185 -15.195   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      52.388 -25.835   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      52.394 -22.485   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      48.775 -24.154   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      48.303 -19.309   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      51.470 -17.260   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      46.409 -31.185   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0      49.200 -26.865   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0      46.409 -26.565   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      45.075 -28.875   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0      49.200 -29.344   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      49.209 -21.444   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      49.678 -25.401   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      49.682 -22.910   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      51.143 -24.928   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      51.146 -23.388   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      47.742 -27.335   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      46.409 -29.645   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      47.742 -28.875   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      45.075 -27.335   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      50.098 -28.105   0.000  0.00  0.00           C+0
CONECT    1    3    4    5   11                                             
CONECT    2    3    6    7   12                                             
CONECT    3    1    2                                                       
CONECT    4    1   18                                                       
CONECT    5    1                                                            
CONECT    6    2                                                            
CONECT    7    2                                                            
CONECT    8   21                                                            
CONECT    9   22                                                            
CONECT   10   19   20                                                       
CONECT   11    1                                                            
CONECT   12    2                                                            
CONECT   13   24                                                            
CONECT   14   19   23   27                                                  
CONECT   15   23   26                                                       
CONECT   16   24   26                                                       
CONECT   17   25   27                                                       
CONECT   18    4   20                                                       
CONECT   19   10   14   21                                                  
CONECT   20   10   18   22                                                  
CONECT   21    8   19   22                                                  
CONECT   22    9   20   21                                                  
CONECT   23   14   15   25                                                  
CONECT   24   13   16   25                                                  
CONECT   25   17   23   24                                                  
CONECT   26   15   16                                                       
CONECT   27   14   17                                                       
MASTER        0    0    0    0    0    0    0    0   27    0   58    0
END

COMPND    HMDB0003335
HETATM    1  O1  UNL     1      -7.037   1.431  -0.705  1.00  0.00           O  
HETATM    2  C1  UNL     1      -5.981   0.801  -0.950  1.00  0.00           C  
HETATM    3  N1  UNL     1      -5.888   0.150  -2.119  1.00  0.00           N  
HETATM    4  C2  UNL     1      -4.760  -0.543  -2.418  1.00  0.00           C  
HETATM    5  N2  UNL     1      -3.753  -0.561  -1.527  1.00  0.00           N  
HETATM    6  C3  UNL     1      -3.798   0.075  -0.342  1.00  0.00           C  
HETATM    7  C4  UNL     1      -4.932   0.773  -0.039  1.00  0.00           C  
HETATM    8  N3  UNL     1      -4.769   1.325   1.176  1.00  0.00           N  
HETATM    9  C5  UNL     1      -3.546   0.961   1.598  1.00  0.00           C  
HETATM   10  N4  UNL     1      -2.934   0.205   0.702  1.00  0.00           N  
HETATM   11  C6  UNL     1      -1.644  -0.431   0.663  1.00  0.00           C  
HETATM   12  O2  UNL     1      -0.886   0.159  -0.317  1.00  0.00           O  
HETATM   13  C7  UNL     1       0.256   0.668   0.229  1.00  0.00           C  
HETATM   14  C8  UNL     1       1.464  -0.209  -0.026  1.00  0.00           C  
HETATM   15  O3  UNL     1       2.617   0.332   0.540  1.00  0.00           O  
HETATM   16  P1  UNL     1       3.967  -0.627   0.269  1.00  0.00           P  
HETATM   17  O4  UNL     1       3.783  -1.926   1.028  1.00  0.00           O  
HETATM   18  O5  UNL     1       5.295   0.159   0.994  1.00  0.00           O  
HETATM   19  O6  UNL     1       4.250  -0.904  -1.374  1.00  0.00           O  
HETATM   20  P2  UNL     1       5.451   0.172  -1.881  1.00  0.00           P  
HETATM   21  O7  UNL     1       4.808   1.560  -1.919  1.00  0.00           O  
HETATM   22  O8  UNL     1       6.062  -0.248  -3.408  1.00  0.00           O  
HETATM   23  O9  UNL     1       6.658   0.211  -0.709  1.00  0.00           O  
HETATM   24  C9  UNL     1       0.062   0.731   1.732  1.00  0.00           C  
HETATM   25  O10 UNL     1      -0.498   1.952   2.030  1.00  0.00           O  
HETATM   26  C10 UNL     1      -0.878  -0.436   1.911  1.00  0.00           C  
HETATM   27  O11 UNL     1      -1.568  -0.436   3.084  1.00  0.00           O  
HETATM   28  H1  UNL     1      -4.736  -1.049  -3.371  1.00  0.00           H  
HETATM   29  H2  UNL     1      -2.908  -1.103  -1.794  1.00  0.00           H  
HETATM   30  H3  UNL     1      -3.099   1.238   2.544  1.00  0.00           H  
HETATM   31  H4  UNL     1      -1.829  -1.492   0.346  1.00  0.00           H  
HETATM   32  H5  UNL     1       0.458   1.695  -0.187  1.00  0.00           H  
HETATM   33  H6  UNL     1       1.621  -0.401  -1.105  1.00  0.00           H  
HETATM   34  H7  UNL     1       1.283  -1.172   0.514  1.00  0.00           H  
HETATM   35  H8  UNL     1       5.146   1.138   0.817  1.00  0.00           H  
HETATM   36  H9  UNL     1       7.033  -0.405  -3.284  1.00  0.00           H  
HETATM   37  H10 UNL     1       7.483  -0.221  -1.096  1.00  0.00           H  
HETATM   38  H11 UNL     1       1.025   0.572   2.264  1.00  0.00           H  
HETATM   39  H12 UNL     1      -0.715   2.492   1.211  1.00  0.00           H  
HETATM   40  H13 UNL     1      -0.215  -1.352   1.914  1.00  0.00           H  
HETATM   41  H14 UNL     1      -2.348  -1.014   3.003  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    4
CONECT    4    5   28
CONECT    5    6   29
CONECT    6    7    7   10
CONECT    7    8
CONECT    8    9    9
CONECT    9   10   30
CONECT   10   11
CONECT   11   12   26   31
CONECT   12   13
CONECT   13   14   24   32
CONECT   14   15   33   34
CONECT   15   16
CONECT   16   17   17   18   19
CONECT   18   35
CONECT   19   20
CONECT   20   21   21   22   23
CONECT   22   36
CONECT   23   37
CONECT   24   25   26   38
CONECT   25   39
CONECT   26   27   40
CONECT   27   41
END

HMDB0003335
     RDKit          3D
IDP
 41 43  0  0  0  0  0  0  0  0999 V2000
   -7.0368    1.4313   -0.7051 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9814    0.8010   -0.9499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8881    0.1500   -2.1193 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7598   -0.5427   -2.4176 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7534   -0.5605   -1.5266 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7984    0.0752   -0.3421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9316    0.7730   -0.0386 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7691    1.3253    1.1759 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5461    0.9609    1.5978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9338    0.2046    0.7023 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6443   -0.4309    0.6632 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8864    0.1591   -0.3172 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2565    0.6675    0.2285 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4642   -0.2087   -0.0258 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6171    0.3318    0.5405 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9673   -0.6267    0.2690 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.7825   -1.9257    1.0276 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2952    0.1593    0.9944 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2497   -0.9036   -1.3738 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4509    0.1723   -1.8813 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.8082    1.5600   -1.9187 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0621   -0.2482   -3.4081 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6577    0.2109   -0.7091 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0615    0.7309    1.7318 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4976    1.9515    2.0297 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8776   -0.4360    1.9113 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5681   -0.4360    3.0837 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7356   -1.0487   -3.3710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9077   -1.1026   -1.7940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0988    1.2380    2.5436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8288   -1.4919    0.3463 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4577    1.6952   -0.1866 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6210   -0.4007   -1.1048 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2834   -1.1720    0.5142 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1464    1.1379    0.8170 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0330   -0.4052   -3.2839 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4827   -0.2206   -1.0957 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0249    0.5719    2.2644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7149    2.4920    1.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2152   -1.3522    1.9139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3484   -1.0143    3.0031 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 20 23  1  0
 13 24  1  0
 24 25  1  0
 24 26  1  0
 26 27  1  0
  7  2  1  0
 26 11  1  0
 10  6  1  0
  4 28  1  0
  5 29  1  0
  9 30  1  0
 11 31  1  0
 13 32  1  6
 14 33  1  0
 14 34  1  0
 18 35  1  0
 22 36  1  0
 23 37  1  0
 24 38  1  1
 25 39  1  0
 26 40  1  6
 27 41  1  0
M  END

Synonyms

Value	Source
5'-IDP	HMDB
Inosine 5'-(trihydrogen diphosphate)	HMDB
Inosine 5'-(trihydrogen pyrophosphate)	HMDB
Inosine 5'-diphosphate	HMDB
Inosine 5'-pyrophosphate	HMDB
Inosine diphosphate	HMDB
Inosine pyrophosphate	HMDB
Riboxin	HMDB
Riboxine	HMDB
Diphosphate, inosine	HMDB
Pyrophosphate, inosine	HMDB

Molecular Formula

C₁₀H₁₄N₄O₁₁P₂

Average Mass

428.1859

Monoisotopic Mass

428.013430334

IUPAC Name

[({[(2R,3S,4R)-3,4-dihydroxy-5-(6-oxo-6,9-dihydro-3H-purin-9-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

{[(2R,3S,4R)-3,4-dihydroxy-5-(6-oxo-3H-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid

CAS Registry Number

86-04-4

SMILES

O[C@@H]1[C@@H](COP(O)(=O)OP(O)(O)=O)OC([C@@H]1O)N1C=NC2=C1NC=NC2=O

InChI Identifier

InChI=1S/C10H14N4O11P2/c15-6-4(1-23-27(21,22)25-26(18,19)20)24-10(7(6)16)14-3-13-5-8(14)11-2-12-9(5)17/h2-4,6-7,10,15-16H,1H2,(H,21,22)(H,11,12,17)(H2,18,19,20)/t4-,6-,7-,10?/m1/s1

InChI Key

JPXZQMKKFWMMGK-VTHZCTBJSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine ribonucleoside diphosphates

Alternative Parents

Substituents

Purine ribonucleoside diphosphate
Purine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
6-oxopurine
Hypoxanthine
Monosaccharide phosphate
Organic pyrophosphate
Imidazopyrimidine
Purine
Monoalkyl phosphate
Pyrimidone
Pyrimidine
Alkyl phosphate
Phosphoric acid ester
Monosaccharide
Organic phosphoric acid derivative
N-substituted imidazole
Tetrahydrofuran
Vinylogous amide
Azole
Imidazole
Heteroaromatic compound
1,2-diol
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Organooxygen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Organonitrogen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	4.26 g/L	ALOGPS
logP	-0.99	ALOGPS
logP	-3.6	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	2.65	ChemAxon
pKa (Strongest Basic)	1.73	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	222.26 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	82.64 m³·mol⁻¹	ChemAxon
Polarizability	33.75 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Extracellular
Mitochondria
Nucleus

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191757	Ectonucleoside triphosphate diphosphohydrolase 1	Unknown	P49961	Homo sapiens
MMDBp0191758	Soluble calcium-activated nucleotidase 1	Unknown	Q8WVQ1	Homo sapiens
MMDBp0191759	Ectonucleoside triphosphate diphosphohydrolase 3	Unknown	O75355	Homo sapiens
MMDBp0191778	Uridine-cytidine kinase 1	Unknown	Q9HA47	Homo sapiens
MMDBp0191779	Nucleoside diphosphate kinase, mitochondrial	Unknown	O00746	Homo sapiens
MMDBp0191781	Nucleoside diphosphate kinase A	Unknown	P15531	Homo sapiens
MMDBp0191782	Nucleoside diphosphate kinase 7	Unknown	Q9Y5B8	Homo sapiens
MMDBp0191784	Nucleoside diphosphate kinase B	Unknown	P22392	Homo sapiens
MMDBp0191785	Nucleoside diphosphate kinase 3	Unknown	Q13232	Homo sapiens
MMDBp0191786	Nucleoside diphosphate kinase 6	Unknown	O75414	Homo sapiens
MMDBp0191880	Glucokinase	Enzyme	P35557	Homo sapiens
MMDBp0191882	Hexokinase-3	Enzyme	P52790	Homo sapiens
MMDBp0191883	Hexokinase-2	Enzyme	P52789	Homo sapiens
MMDBp0192369	6-phosphofructokinase type C	Unknown	Q01813	Homo sapiens
MMDBp0192381	6-phosphofructokinase, liver type	Unknown	P17858	Homo sapiens
MMDBp0192384	6-phosphofructokinase, muscle type	Unknown	P08237	Homo sapiens
MMDBp0192385	Pyruvate kinase isozymes M1/M2	Unknown	P14618	Homo sapiens
MMDBp0192387	Pyruvate kinase isozymes R/L	Unknown	P30613	Homo sapiens
MMDBp0192495	Ectonucleoside triphosphate diphosphohydrolase 4	Unknown	Q9Y227	Homo sapiens
MMDBp0192496	Ectonucleoside triphosphate diphosphohydrolase 6	Unknown	O75354	Homo sapiens
MMDBp0192497	Ectonucleoside triphosphate diphosphohydrolase 5	Unknown	O75356	Homo sapiens
MMDBp0192507	Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial	Unknown	P53597	Homo sapiens
MMDBp0192508	Phosphoenolpyruvate carboxykinase [GTP], mitochondrial	Unknown	Q16822	Homo sapiens
MMDBp0192509	Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial	Unknown	Q96I99	Homo sapiens
MMDBp0192510	Phosphoenolpyruvate carboxykinase, cytosolic [GTP]	Unknown	P35558	Homo sapiens
MMDBp0192583	Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial	Unknown	Q9P2R7	Homo sapiens
MMDBp0193590	Uridine-cytidine kinase 2	Unknown	Q9BZX2	Homo sapiens
MMDBp0193868	ENTPD4 protein	Enzyme	Q8NE73	Homo sapiens
MMDBp0194185	Uridine-cytidine kinase-like 1	Enzyme	Q9NWZ5	Homo sapiens
MMDBp0194442	Ectonucleoside triphosphate diphosphohydrolase 8	Unknown	Q5MY95	Homo sapiens
MMDBp0196906	Nucleoside diphosphate kinase homolog 5	Unknown	P56597

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Proteobacteria	226	Human ; Human sputum; Human subgingival plaque; Human feces; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	364	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle ; Human stool	Metabolic reconstruction
Bacteria	Actinobacteria	15	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human subgingival plaque; Human mucosa; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	113	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human subgingival plaque; Human mucosa; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	126	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	28	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle ; Human stool	Metabolic reconstruction
Bacteria	Proteobacteria	9	Human ; Human sputum; Human subgingival plaque; Human feces; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	4	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	8		Metabolic reconstruction
Archaea/Archaea	Crenarchaeota	14		Metabolic reconstruction
Archaea/Archaea	Korarchaeota	1
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0003335

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023146

KNApSAcK ID

Not Available

Chemspider ID

559208

KEGG Compound ID

C00104

BioCyc ID

Not Available

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

17808

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Hlushko LV, Makovets'ka TI, Neiko IeM: [The dynamics of the glycocholic acid content of the bile in patients with chronic inactive hepatitis]. Lik Sprava. 1995 May-Jun;(5-6):152-4. [PubMed:8630789 ]

Showing metabocard for IDP (MMDBc0032840)

MOL for #<Metabolite:0x00007f9222dbcf20>

3D MOL for #<Metabolite:0x00007f9222dbcf20>

3D SDF for #<Metabolite:0x00007f9222dbcf20>

3D-SDF for #<Metabolite:0x00007f9222dbcf20>

PDB for #<Metabolite:0x00007f9222dbcf20>

3D PDB for #<Metabolite:0x00007f9222dbcf20>

SMILES for #<Metabolite:0x00007f9222dbcf20>

INCHI for #<Metabolite:0x00007f9222dbcf20>

Structure for #<Metabolite:0x00007f9222dbcf20>

3D Structure for #<Metabolite:0x00007f9222dbcf20>