Showing metabocard for 8-oxo-dGDP (MMDBc0054308)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 23:06:17 UTC
Update Date2022-09-01 02:28:24 UTC
Metabolite IDMMDBc0054308
Metabolite Identification
Common Name8-oxo-dGDP
Description8-oxo-dGDP belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. 8-oxo-dGDP is a very strong basic compound (based on its pKa). In humans, 8-oxo-dGDP is involved in the metabolic disorder called the purine nucleoside phosphorylase deficiency pathway. 8-oxo-dgdp is part of the Purine metabolism pathway.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645c9426228>


  Mrv0541 10301209532D          

 31 33  0  0  0  0            999 V2000
   -1.1831   -2.4049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -4.2695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -3.2299    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3984   -3.4849    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3984   -2.1500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505   -3.7149    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534   -0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7873   -6.3533    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8088   -6.9888    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1518   -5.3748    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1338   -5.4806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7030   -4.9707    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6635   -4.4410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0865   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1733   -6.0103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9803   -6.1818    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.9184   -5.2257    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9181   -2.8554    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9818   -4.0682    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9818   -1.5666    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  6  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  7  6  2  0  0  0  0
  8  6  1  0  0  0  0
 11  9  2  0  0  0  0
 12  6  1  0  0  0  0
 12 10  2  0  0  0  0
 13  7  1  0  0  0  0
 13  9  1  0  0  0  0
 14  8  2  0  0  0  0
 14  9  1  0  0  0  0
  5 15  1  6  0  0  0
 15  7  1  0  0  0  0
 15 10  1  0  0  0  0
  3 16  1  1  0  0  0
 17  8  1  0  0  0  0
 18 10  1  0  0  0  0
 24  2  1  0  0  0  0
 25  4  1  0  0  0  0
 25  5  1  0  0  0  0
 27 19  1  0  0  0  0
 27 20  1  0  0  0  0
 27 21  2  0  0  0  0
 27 26  1  0  0  0  0
 28 22  1  0  0  0  0
 28 23  2  0  0  0  0
 28 24  1  0  0  0  0
 28 26  1  0  0  0  0
  3 29  1  6  0  0  0
  4 30  1  1  0  0  0
  5 31  1  1  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00005645c9426228>

HMDB0059648
     RDKit          3D
8-oxo-dGDP
 43 45  0  0  0  0  0  0  0  0999 V2000
   -6.2188    0.5436   -2.8321 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7263    0.2286   -1.6573 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5110   -0.2224   -0.6607 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0816   -0.5602    0.5538 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9248   -1.0241    1.5624 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7338   -0.4443    0.8244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9944   -0.6933    1.9142 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7166   -0.3983    1.6135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5887   -0.4931    2.4177 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6698    0.0315    0.3414 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4905    0.4539   -0.3877 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7613    1.5725    0.3164 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6162    1.4691   -0.3516 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6802    2.2665   -1.4887 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6819    0.0221   -0.6929 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7770   -0.6830    0.1020 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9861   -0.0342   -0.1430 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2653   -0.7243    0.6804 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.8052   -1.5767    1.8518 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2069    0.5303    1.3276 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2497   -1.6725   -0.3169 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5889   -0.8047   -0.8719 P   0  0  0  0  0  5  0  0  0  0  0  0
    6.1997    0.0495   -2.0721 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8011   -1.8653   -1.3942 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2083    0.1439    0.3794 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5466   -0.5467   -0.5151 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9189    0.0204   -0.1996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4109    0.3461   -1.4064 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2482    0.4260   -2.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7285   -1.9392    1.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5257    0.0827    3.2684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7432    0.8229   -1.3994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5795    1.3454    1.3865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2180    2.5613    0.1467 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4040    1.7762    0.3760 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4372    1.9052   -2.0381 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9589   -0.0648   -1.7795 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5435   -0.5467    1.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8087   -1.7603   -0.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1585    1.2908    0.6684 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5147   -2.7978   -1.2131 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1746    0.2770    0.3043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7297    0.6863   -2.1173 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 18 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
 10 27  1  0
 27 28  1  0
 28  2  1  0
 27  6  2  0
 26 11  1  0
  1 29  1  0
  5 30  1  0
  9 31  1  0
 11 32  1  6
 12 33  1  0
 12 34  1  0
 13 35  1  1
 14 36  1  0
 15 37  1  6
 16 38  1  0
 16 39  1  0
 20 40  1  0
 24 41  1  0
 25 42  1  0
 28 43  1  0
M  END
Download

3D SDF for #<Metabolite:0x00005645c9426228>


  Mrv0541 10301209532D          

 31 33  0  0  0  0            999 V2000
   -1.1831   -2.4049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -4.2695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -3.2299    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3984   -3.4849    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3984   -2.1500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505   -3.7149    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534   -0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7873   -6.3533    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8088   -6.9888    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1518   -5.3748    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1338   -5.4806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7030   -4.9707    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6635   -4.4410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0865   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1733   -6.0103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9803   -6.1818    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.9184   -5.2257    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9181   -2.8554    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9818   -4.0682    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9818   -1.5666    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  6  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  7  6  2  0  0  0  0
  8  6  1  0  0  0  0
 11  9  2  0  0  0  0
 12  6  1  0  0  0  0
 12 10  2  0  0  0  0
 13  7  1  0  0  0  0
 13  9  1  0  0  0  0
 14  8  2  0  0  0  0
 14  9  1  0  0  0  0
  5 15  1  6  0  0  0
 15  7  1  0  0  0  0
 15 10  1  0  0  0  0
  3 16  1  1  0  0  0
 17  8  1  0  0  0  0
 18 10  1  0  0  0  0
 24  2  1  0  0  0  0
 25  4  1  0  0  0  0
 25  5  1  0  0  0  0
 27 19  1  0  0  0  0
 27 20  1  0  0  0  0
 27 21  2  0  0  0  0
 27 26  1  0  0  0  0
 28 22  1  0  0  0  0
 28 23  2  0  0  0  0
 28 24  1  0  0  0  0
 28 26  1  0  0  0  0
  3 29  1  6  0  0  0
  4 30  1  1  0  0  0
  5 31  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054308

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)C[C@@]([H])(O[C@]1([H])COP(O)(=O)OP(O)(O)=O)N1C(O)=NC2=C1NC(=N)N=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N5O11P2/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(25-5)2-24-28(22,23)26-27(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1

> <INCHI_KEY>
LJMLTZSNWOCYNQ-VPENINKCSA-N

> <FORMULA>
C10H15N5O11P2

> <MOLECULAR_WEIGHT>
443.2005

> <EXACT_MASS>
443.024329371

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
34.87022991256715

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[(2R,3S,5R)-5-(6,8-dihydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <ALOGPS_LOGP>
-1.45

> <JCHEM_LOGP>
-1.8732008885516371

> <ALOGPS_LOGS>
-1.90

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.110682200715929

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7716579176866856

> <JCHEM_PKA_STRONGEST_BASIC>
5.363617962357166

> <JCHEM_POLAR_SURFACE_AREA>
249.26999999999995

> <JCHEM_REFRACTIVITY>
96.89149999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.62e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{[(2R,3S,5R)-5-(6,8-dihydroxy-2-imino-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00005645c9426228>

HMDB0059648
     RDKit          3D
8-oxo-dGDP
 43 45  0  0  0  0  0  0  0  0999 V2000
   -6.2188    0.5436   -2.8321 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7263    0.2286   -1.6573 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5110   -0.2224   -0.6607 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0816   -0.5602    0.5538 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9248   -1.0241    1.5624 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7338   -0.4443    0.8244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9944   -0.6933    1.9142 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7166   -0.3983    1.6135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5887   -0.4931    2.4177 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6698    0.0315    0.3414 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4905    0.4539   -0.3877 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7613    1.5725    0.3164 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6162    1.4691   -0.3516 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6802    2.2665   -1.4887 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6819    0.0221   -0.6929 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7770   -0.6830    0.1020 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9861   -0.0342   -0.1430 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2653   -0.7243    0.6804 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.8052   -1.5767    1.8518 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2069    0.5303    1.3276 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2497   -1.6725   -0.3169 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5889   -0.8047   -0.8719 P   0  0  0  0  0  5  0  0  0  0  0  0
    6.1997    0.0495   -2.0721 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8011   -1.8653   -1.3942 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2083    0.1439    0.3794 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5466   -0.5467   -0.5151 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9189    0.0204   -0.1996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4109    0.3461   -1.4064 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2482    0.4260   -2.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7285   -1.9392    1.9516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5257    0.0827    3.2684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7432    0.8229   -1.3994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5795    1.3454    1.3865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2180    2.5613    0.1467 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4040    1.7762    0.3760 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4372    1.9052   -2.0381 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9589   -0.0648   -1.7795 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5435   -0.5467    1.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8087   -1.7603   -0.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1585    1.2908    0.6684 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5147   -2.7978   -1.2131 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1746    0.2770    0.3043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7297    0.6863   -2.1173 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 18 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
 10 27  1  0
 27 28  1  0
 28  2  1  0
 27  6  2  0
 26 11  1  0
  1 29  1  0
  5 30  1  0
  9 31  1  0
 11 32  1  6
 12 33  1  0
 12 34  1  0
 13 35  1  1
 14 36  1  0
 15 37  1  6
 16 38  1  0
 16 39  1  0
 20 40  1  0
 24 41  1  0
 25 42  1  0
 28 43  1  0
M  END
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PDB for #<Metabolite:0x00005645c9426228>

HEADER    PROTEIN                                 30-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-OCT-12         0                                  
HETATM    1  C   UNK     0      -2.208  -4.489   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.268  -7.970   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.208  -6.029   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.744  -6.505   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.744  -4.013   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.530   0.237   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.864  -2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       5.198  -2.843   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       2.530  -2.843   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       3.864  -0.533   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0      -0.268  -2.549   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0      -3.454  -6.934   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.530   1.777   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -2.713  -1.303   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       5.203 -11.859   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       3.376 -13.046   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       4.017 -10.033   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.250 -10.230   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       3.179  -9.279   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.239  -8.290   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.161  -5.259   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       2.190 -11.219   0.000  0.00  0.00           O+0
HETATM   27  P   UNK     0       3.697 -11.539   0.000  0.00  0.00           P+0
HETATM   28  P   UNK     0       1.714  -9.755   0.000  0.00  0.00           P+0
HETATM   29  H   UNK     0      -3.580  -5.330   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0      -1.833  -7.594   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0      -1.833  -2.924   0.000  0.00  0.00           H+0
CONECT    1    3    5                                                       
CONECT    2    4   24                                                       
CONECT    3    1    4   16   29                                             
CONECT    4    2    3   25   30                                             
CONECT    5    1   15   25   31                                             
CONECT    6    7    8   12                                                  
CONECT    7    6   13   15                                                  
CONECT    8    6   14   17                                                  
CONECT    9   11   13   14                                                  
CONECT   10   12   15   18                                                  
CONECT   11    9                                                            
CONECT   12    6   10                                                       
CONECT   13    7    9                                                       
CONECT   14    8    9                                                       
CONECT   15    5    7   10                                                  
CONECT   16    3                                                            
CONECT   17    8                                                            
CONECT   18   10                                                            
CONECT   19   27                                                            
CONECT   20   27                                                            
CONECT   21   27                                                            
CONECT   22   28                                                            
CONECT   23   28                                                            
CONECT   24    2   28                                                       
CONECT   25    4    5                                                       
CONECT   26   27   28                                                       
CONECT   27   19   20   21   26                                             
CONECT   28   22   23   24   26                                             
CONECT   29    3                                                            
CONECT   30    4                                                            
CONECT   31    5                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END
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3D PDB for #<Metabolite:0x00005645c9426228>

COMPND    HMDB0059648
HETATM    1  N1  UNL     1      -6.219   0.544  -2.832  1.00  0.00           N  
HETATM    2  C1  UNL     1      -5.726   0.229  -1.657  1.00  0.00           C  
HETATM    3  N2  UNL     1      -6.511  -0.222  -0.661  1.00  0.00           N  
HETATM    4  C2  UNL     1      -6.082  -0.560   0.554  1.00  0.00           C  
HETATM    5  O1  UNL     1      -6.925  -1.024   1.562  1.00  0.00           O  
HETATM    6  C3  UNL     1      -4.734  -0.444   0.824  1.00  0.00           C  
HETATM    7  N3  UNL     1      -3.994  -0.693   1.914  1.00  0.00           N  
HETATM    8  C4  UNL     1      -2.717  -0.398   1.614  1.00  0.00           C  
HETATM    9  O2  UNL     1      -1.589  -0.493   2.418  1.00  0.00           O  
HETATM   10  N4  UNL     1      -2.670   0.031   0.341  1.00  0.00           N  
HETATM   11  C5  UNL     1      -1.491   0.454  -0.388  1.00  0.00           C  
HETATM   12  C6  UNL     1      -0.761   1.572   0.316  1.00  0.00           C  
HETATM   13  C7  UNL     1       0.616   1.469  -0.352  1.00  0.00           C  
HETATM   14  O3  UNL     1       0.680   2.267  -1.489  1.00  0.00           O  
HETATM   15  C8  UNL     1       0.682   0.022  -0.693  1.00  0.00           C  
HETATM   16  C9  UNL     1       1.777  -0.683   0.102  1.00  0.00           C  
HETATM   17  O4  UNL     1       2.986  -0.034  -0.143  1.00  0.00           O  
HETATM   18  P1  UNL     1       4.265  -0.724   0.680  1.00  0.00           P  
HETATM   19  O5  UNL     1       3.805  -1.577   1.852  1.00  0.00           O  
HETATM   20  O6  UNL     1       5.207   0.530   1.328  1.00  0.00           O  
HETATM   21  O7  UNL     1       5.250  -1.672  -0.317  1.00  0.00           O  
HETATM   22  P2  UNL     1       6.589  -0.805  -0.872  1.00  0.00           P  
HETATM   23  O8  UNL     1       6.200   0.050  -2.072  1.00  0.00           O  
HETATM   24  O9  UNL     1       7.801  -1.865  -1.394  1.00  0.00           O  
HETATM   25  O10 UNL     1       7.208   0.144   0.379  1.00  0.00           O  
HETATM   26  O11 UNL     1      -0.547  -0.547  -0.515  1.00  0.00           O  
HETATM   27  C10 UNL     1      -3.919   0.020  -0.200  1.00  0.00           C  
HETATM   28  N5  UNL     1      -4.411   0.346  -1.406  1.00  0.00           N  
HETATM   29  H1  UNL     1      -7.248   0.426  -2.952  1.00  0.00           H  
HETATM   30  H2  UNL     1      -6.728  -1.939   1.952  1.00  0.00           H  
HETATM   31  H3  UNL     1      -1.526   0.083   3.268  1.00  0.00           H  
HETATM   32  H4  UNL     1      -1.743   0.823  -1.399  1.00  0.00           H  
HETATM   33  H5  UNL     1      -0.579   1.345   1.386  1.00  0.00           H  
HETATM   34  H6  UNL     1      -1.218   2.561   0.147  1.00  0.00           H  
HETATM   35  H7  UNL     1       1.404   1.776   0.376  1.00  0.00           H  
HETATM   36  H8  UNL     1       1.437   1.905  -2.038  1.00  0.00           H  
HETATM   37  H9  UNL     1       0.959  -0.065  -1.779  1.00  0.00           H  
HETATM   38  H10 UNL     1       1.544  -0.547   1.179  1.00  0.00           H  
HETATM   39  H11 UNL     1       1.809  -1.760  -0.149  1.00  0.00           H  
HETATM   40  H12 UNL     1       5.159   1.291   0.668  1.00  0.00           H  
HETATM   41  H13 UNL     1       7.515  -2.798  -1.213  1.00  0.00           H  
HETATM   42  H14 UNL     1       8.175   0.277   0.304  1.00  0.00           H  
HETATM   43  H15 UNL     1      -3.730   0.686  -2.117  1.00  0.00           H  
CONECT    1    2    2   29
CONECT    2    3   28
CONECT    3    4    4
CONECT    4    5    6
CONECT    5   30
CONECT    6    7   27   27
CONECT    7    8    8
CONECT    8    9   10
CONECT    9   31
CONECT   10   11   27
CONECT   11   12   26   32
CONECT   12   13   33   34
CONECT   13   14   15   35
CONECT   14   36
CONECT   15   16   26   37
CONECT   16   17   38   39
CONECT   17   18
CONECT   18   19   19   20   21
CONECT   20   40
CONECT   21   22
CONECT   22   23   23   24   25
CONECT   24   41
CONECT   25   42
CONECT   27   28
CONECT   28   43
END
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SMILES for #<Metabolite:0x00005645c9426228>

[H][C@]1(O)C[C@@]([H])(O[C@]1([H])COP(O)(=O)OP(O)(O)=O)N1C(O)=NC2=C1NC(=N)N=C2O
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INCHI for #<Metabolite:0x00005645c9426228>

InChI=1S/C10H15N5O11P2/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(25-5)2-24-28(22,23)26-27(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
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Synonyms
ValueSource
2'-Deoxy-8-oxo-guanosine-5'-diphosphateChEBI
8-oxo-2'-Deoxyguanosine-5'-diphosphateChEBI
8-Oxodeoxyguanosine diphosphateChEBI
2'-Deoxy-8-oxo-guanosine-5'-diphosphoric acidGenerator
8-oxo-2'-Deoxyguanosine-5'-diphosphoric acidGenerator
8-Oxodeoxyguanosine diphosphoric acidGenerator
2'-Deoxy-7,8-dihydro-8-oxoguanosine diphosphateHMDB
8-oxo-7,8-Dihydrodeoxyguanosine diphosphateHMDB
Molecular FormulaC10H15N5O11P2
Average Mass443.2005
Monoisotopic Mass443.024329371
IUPAC Name[({[(2R,3S,5R)-5-(6,8-dihydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional Name{[(2R,3S,5R)-5-(6,8-dihydroxy-2-imino-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
[H][C@]1(O)C[C@@]([H])(O[C@]1([H])COP(O)(=O)OP(O)(O)=O)N1C(O)=NC2=C1NC(=N)N=C2O
InChI Identifier
InChI=1S/C10H15N5O11P2/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(25-5)2-24-28(22,23)26-27(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
InChI KeyLJMLTZSNWOCYNQ-VPENINKCSA-N