MiMeDB: Showing metabocard for 2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone (MMDBc0032981)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:29:48 UTC

Update Date

2022-08-31 21:54:51 UTC

Metabolite ID

MMDBc0032981

Metabolite Identification

Common Name

2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone

Description

2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone, also known as 2,5-diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate, belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit. 2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on 2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone.

Structure

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

HMDB0304043
     RDKit          3D
2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one
 41 41  0  0  0  0  0  0  0  0999 V2000
   -4.6564    1.7893    2.3195 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5046    0.8152    1.2870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3152    0.5061    0.7529 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1740   -0.4232   -0.2314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9081   -0.7365   -0.7836 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7174   -0.0632   -0.3043 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5171   -0.5437   -1.0233 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6404   -1.9116   -0.7958 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6892    0.2318   -0.4983 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5080    1.5753   -0.7534 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9973   -0.2438   -1.0948 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1671   -1.6078   -0.8281 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1339    0.5389   -0.4720 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1494    0.3419    0.8989 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3842    1.1807    1.6520 P   0  0  0  0  0  5  0  0  0  0  0  0
    6.4038    0.1744    2.1360 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7631    2.0336    2.9974 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0659    2.3241    0.6129 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2893   -1.0648   -0.6917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1765   -2.0396   -1.7179 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5259   -0.7549   -0.1483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5585   -1.3637   -0.5897 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5920    0.1672    0.8151 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3363    2.7677    2.1850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0959    1.4856    3.2047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8420   -1.4507   -1.5325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5816   -0.2192    0.7910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8816    1.0334   -0.4862 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4303   -0.3446   -2.1056 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9101   -2.1029    0.1290 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7068    0.1014    0.6020 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8458    1.6759   -1.4901 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9695   -0.1093   -2.1944 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0757   -1.9022   -1.0325 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0890    0.1406   -0.9073 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0729    1.5947   -0.7724 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8250    1.7505    3.1723 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6088    1.9234   -0.1002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1543   -3.0715   -1.5039 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1104   -1.7939   -2.7243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5335    0.4007    1.2264 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
  4 19  2  0
 19 20  1  0
 19 21  1  0
 21 22  2  0
 21 23  1  0
 23  2  1  0
  1 24  1  0
  1 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  7 29  1  6
  8 30  1  0
  9 31  1  1
 10 32  1  0
 11 33  1  6
 12 34  1  0
 13 35  1  0
 13 36  1  0
 17 37  1  0
 18 38  1  0
 20 39  1  0
 20 40  1  0
 23 41  1  0
M  END

Structure #1
  Mrv0541 02241222182D          

 23 23  0  0  0  0            999 V2000
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9293   -0.7969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1 12  1  0  0  0  0
  2  4  1  0  0  0  0
  2 19  1  0  0  0  0
  3  6  1  0  0  0  0
  3 15  1  6  0  0  0
  4  6  1  0  0  0  0
  4 16  1  6  0  0  0
  5  7  2  0  0  0  0
  5  8  1  0  0  0  0
  5 10  1  0  0  0  0
  6 17  1  1  0  0  0
  7 12  1  0  0  0  0
  7 13  1  0  0  0  0
  8 14  1  0  0  0  0
  8 18  2  0  0  0  0
  9 11  1  0  0  0  0
  9 13  2  0  0  0  0
  9 14  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 20 23  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032981

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC(NC[C@H](O)[C@H](O)[C@H](O)COP(O)(O)=O)=C(N)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C9H18N5O8P/c10-5-7(13-9(11)14-8(5)18)12-1-3(15)6(17)4(16)2-22-23(19,20)21/h3-4,6,15-17H,1-2,10H2,(H2,19,20,21)(H4,11,12,13,14,18)/t3-,4+,6-/m0/s1

> <INCHI_KEY>
ACIVVGBVOVHFPQ-RPDRRWSUSA-N

> <FORMULA>
C9H18N5O8P

> <MOLECULAR_WEIGHT>
355.2417

> <EXACT_MASS>
355.089299089

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
30.981445578498153

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4S)-5-[(2,5-diamino-6-oxo-1,6-dihydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-2.55

> <JCHEM_LOGP>
-4.862116433190331

> <ALOGPS_LOGS>
-1.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.433837913528673

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4915912940964366

> <JCHEM_PKA_STRONGEST_BASIC>
6.521472579895389

> <JCHEM_POLAR_SURFACE_AREA>
232.97999999999993

> <JCHEM_REFRACTIVITY>
84.53669999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.13e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S)-5-[(2,5-diamino-6-oxo-1H-pyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0304043
     RDKit          3D
2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one
 41 41  0  0  0  0  0  0  0  0999 V2000
   -4.6564    1.7893    2.3195 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5046    0.8152    1.2870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3152    0.5061    0.7529 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1740   -0.4232   -0.2314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9081   -0.7365   -0.7836 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7174   -0.0632   -0.3043 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5171   -0.5437   -1.0233 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6404   -1.9116   -0.7958 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6892    0.2318   -0.4983 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5080    1.5753   -0.7534 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9973   -0.2438   -1.0948 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1671   -1.6078   -0.8281 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1339    0.5389   -0.4720 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1494    0.3419    0.8989 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3842    1.1807    1.6520 P   0  0  0  0  0  5  0  0  0  0  0  0
    6.4038    0.1744    2.1360 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7631    2.0336    2.9974 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0659    2.3241    0.6129 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2893   -1.0648   -0.6917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1765   -2.0396   -1.7179 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5259   -0.7549   -0.1483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5585   -1.3637   -0.5897 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5920    0.1672    0.8151 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3363    2.7677    2.1850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0959    1.4856    3.2047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8420   -1.4507   -1.5325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5816   -0.2192    0.7910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8816    1.0334   -0.4862 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4303   -0.3446   -2.1056 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9101   -2.1029    0.1290 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7068    0.1014    0.6020 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8458    1.6759   -1.4901 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9695   -0.1093   -2.1944 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0757   -1.9022   -1.0325 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0890    0.1406   -0.9073 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0729    1.5947   -0.7724 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8250    1.7505    3.1723 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6088    1.9234   -0.1002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1543   -3.0715   -1.5039 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1104   -1.7939   -2.7243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5335    0.4007    1.2264 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
  4 19  2  0
 19 20  1  0
 19 21  1  0
 21 22  2  0
 21 23  1  0
 23  2  1  0
  1 24  1  0
  1 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  7 29  1  6
  8 30  1  0
  9 31  1  1
 10 32  1  0
 11 33  1  6
 12 34  1  0
 13 35  1  0
 13 36  1  0
 17 37  1  0
 18 38  1  0
 20 39  1  0
 20 40  1  0
 23 41  1  0
M  END

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -8.002   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -5.335   1.540   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   20  P   UNK     0     -10.669   0.000   0.000  0.00  0.00           P+0
HETATM   21  O   UNK     0     -12.003  -0.770   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0     -10.669   1.540   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0     -11.068  -1.488   0.000  0.00  0.00           O+0
CONECT    1    3   12                                                       
CONECT    2    4   19                                                       
CONECT    3    1    6   15                                                  
CONECT    4    2    6   16                                                  
CONECT    5    7    8   10                                                  
CONECT    6    3    4   17                                                  
CONECT    7    5   12   13                                                  
CONECT    8    5   14   18                                                  
CONECT    9   11   13   14                                                  
CONECT   10    5                                                            
CONECT   11    9                                                            
CONECT   12    1    7                                                       
CONECT   13    7    9                                                       
CONECT   14    8    9                                                       
CONECT   15    3                                                            
CONECT   16    4                                                            
CONECT   17    6                                                            
CONECT   18    8                                                            
CONECT   19    2   20                                                       
CONECT   20   19   21   22   23                                             
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   20                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

COMPND    HMDB0304043
HETATM    1  N1  UNL     1      -4.656   1.789   2.320  1.00  0.00           N  
HETATM    2  C1  UNL     1      -4.505   0.815   1.287  1.00  0.00           C  
HETATM    3  N2  UNL     1      -3.315   0.506   0.753  1.00  0.00           N  
HETATM    4  C2  UNL     1      -3.174  -0.423  -0.231  1.00  0.00           C  
HETATM    5  N3  UNL     1      -1.908  -0.736  -0.784  1.00  0.00           N  
HETATM    6  C3  UNL     1      -0.717  -0.063  -0.304  1.00  0.00           C  
HETATM    7  C4  UNL     1       0.517  -0.544  -1.023  1.00  0.00           C  
HETATM    8  O1  UNL     1       0.640  -1.912  -0.796  1.00  0.00           O  
HETATM    9  C5  UNL     1       1.689   0.232  -0.498  1.00  0.00           C  
HETATM   10  O2  UNL     1       1.508   1.575  -0.753  1.00  0.00           O  
HETATM   11  C6  UNL     1       2.997  -0.244  -1.095  1.00  0.00           C  
HETATM   12  O3  UNL     1       3.167  -1.608  -0.828  1.00  0.00           O  
HETATM   13  C7  UNL     1       4.134   0.539  -0.472  1.00  0.00           C  
HETATM   14  O4  UNL     1       4.149   0.342   0.899  1.00  0.00           O  
HETATM   15  P1  UNL     1       5.384   1.181   1.652  1.00  0.00           P  
HETATM   16  O5  UNL     1       6.404   0.174   2.136  1.00  0.00           O  
HETATM   17  O6  UNL     1       4.763   2.034   2.997  1.00  0.00           O  
HETATM   18  O7  UNL     1       6.066   2.324   0.613  1.00  0.00           O  
HETATM   19  C8  UNL     1      -4.289  -1.065  -0.692  1.00  0.00           C  
HETATM   20  N4  UNL     1      -4.177  -2.040  -1.718  1.00  0.00           N  
HETATM   21  C9  UNL     1      -5.526  -0.755  -0.148  1.00  0.00           C  
HETATM   22  O8  UNL     1      -6.559  -1.364  -0.590  1.00  0.00           O  
HETATM   23  N5  UNL     1      -5.592   0.167   0.815  1.00  0.00           N  
HETATM   24  H1  UNL     1      -4.336   2.768   2.185  1.00  0.00           H  
HETATM   25  H2  UNL     1      -5.096   1.486   3.205  1.00  0.00           H  
HETATM   26  H3  UNL     1      -1.842  -1.451  -1.533  1.00  0.00           H  
HETATM   27  H4  UNL     1      -0.582  -0.219   0.791  1.00  0.00           H  
HETATM   28  H5  UNL     1      -0.882   1.033  -0.486  1.00  0.00           H  
HETATM   29  H6  UNL     1       0.430  -0.345  -2.106  1.00  0.00           H  
HETATM   30  H7  UNL     1       0.910  -2.103   0.129  1.00  0.00           H  
HETATM   31  H8  UNL     1       1.707   0.101   0.602  1.00  0.00           H  
HETATM   32  H9  UNL     1       0.846   1.676  -1.490  1.00  0.00           H  
HETATM   33  H10 UNL     1       2.969  -0.109  -2.194  1.00  0.00           H  
HETATM   34  H11 UNL     1       4.076  -1.902  -1.033  1.00  0.00           H  
HETATM   35  H12 UNL     1       5.089   0.141  -0.907  1.00  0.00           H  
HETATM   36  H13 UNL     1       4.073   1.595  -0.772  1.00  0.00           H  
HETATM   37  H14 UNL     1       3.825   1.750   3.172  1.00  0.00           H  
HETATM   38  H15 UNL     1       6.609   1.923  -0.100  1.00  0.00           H  
HETATM   39  H16 UNL     1      -4.154  -3.072  -1.504  1.00  0.00           H  
HETATM   40  H17 UNL     1      -4.110  -1.794  -2.724  1.00  0.00           H  
HETATM   41  H18 UNL     1      -6.534   0.401   1.226  1.00  0.00           H  
CONECT    1    2   24   25
CONECT    2    3    3   23
CONECT    3    4
CONECT    4    5   19   19
CONECT    5    6   26
CONECT    6    7   27   28
CONECT    7    8    9   29
CONECT    8   30
CONECT    9   10   11   31
CONECT   10   32
CONECT   11   12   13   33
CONECT   12   34
CONECT   13   14   35   36
CONECT   14   15
CONECT   15   16   16   17   18
CONECT   17   37
CONECT   18   38
CONECT   19   20   21
CONECT   20   39   40
CONECT   21   22   22   23
CONECT   23   41
END

HMDB0304043
     RDKit          3D
2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one
 41 41  0  0  0  0  0  0  0  0999 V2000
   -4.6564    1.7893    2.3195 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5046    0.8152    1.2870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3152    0.5061    0.7529 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1740   -0.4232   -0.2314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9081   -0.7365   -0.7836 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7174   -0.0632   -0.3043 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5171   -0.5437   -1.0233 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6404   -1.9116   -0.7958 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6892    0.2318   -0.4983 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5080    1.5753   -0.7534 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9973   -0.2438   -1.0948 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1671   -1.6078   -0.8281 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1339    0.5389   -0.4720 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1494    0.3419    0.8989 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3842    1.1807    1.6520 P   0  0  0  0  0  5  0  0  0  0  0  0
    6.4038    0.1744    2.1360 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7631    2.0336    2.9974 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0659    2.3241    0.6129 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2893   -1.0648   -0.6917 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1765   -2.0396   -1.7179 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5259   -0.7549   -0.1483 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5585   -1.3637   -0.5897 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5920    0.1672    0.8151 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3363    2.7677    2.1850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0959    1.4856    3.2047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8420   -1.4507   -1.5325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5816   -0.2192    0.7910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8816    1.0334   -0.4862 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4303   -0.3446   -2.1056 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9101   -2.1029    0.1290 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7068    0.1014    0.6020 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8458    1.6759   -1.4901 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9695   -0.1093   -2.1944 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0757   -1.9022   -1.0325 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0890    0.1406   -0.9073 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0729    1.5947   -0.7724 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8250    1.7505    3.1723 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6088    1.9234   -0.1002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1543   -3.0715   -1.5039 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1104   -1.7939   -2.7243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5335    0.4007    1.2264 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
 15 18  1  0
  4 19  2  0
 19 20  1  0
 19 21  1  0
 21 22  2  0
 21 23  1  0
 23  2  1  0
  1 24  1  0
  1 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  7 29  1  6
  8 30  1  0
  9 31  1  1
 10 32  1  0
 11 33  1  6
 12 34  1  0
 13 35  1  0
 13 36  1  0
 17 37  1  0
 18 38  1  0
 20 39  1  0
 20 40  1  0
 23 41  1  0
M  END

Synonyms

Value	Source
2,5-Diamino-6-(1-D-ribitylamino)-4(3H)-pyrimidinone 5'-phosphate	ChEBI
2,5-Diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate	ChEBI
2,5-Diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one	ChEBI
2,5-Diamino-6-(1-D-ribitylamino)-4(3H)-pyrimidinone 5'-phosphoric acid	Generator
2,5-Diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphoric acid	Generator

Molecular Formula

C₉H₁₈N₅O₈P

Average Mass

355.2417

Monoisotopic Mass

355.089299089

IUPAC Name

{[(2R,3S,4S)-5-[(2,5-diamino-6-oxo-1,6-dihydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl]oxy}phosphonic acid

Traditional Name

[(2R,3S,4S)-5-[(2,5-diamino-6-oxo-1H-pyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

NC1=NC(NC[C@H](O)[C@H](O)[C@H](O)COP(O)(O)=O)=C(N)C(=O)N1

InChI Identifier

InChI=1S/C9H18N5O8P/c10-5-7(13-9(11)14-8(5)18)12-1-3(15)6(17)4(16)2-22-23(19,20)21/h3-4,6,15-17H,1-2,10H2,(H2,19,20,21)(H4,11,12,13,14,18)/t3-,4+,6-/m0/s1

InChI Key

ACIVVGBVOVHFPQ-RPDRRWSUSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Monosaccharide phosphate
Aminopyrimidine
Monoalkyl phosphate
Pyrimidone
Secondary aliphatic/aromatic amine
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Vinylogous amide
Secondary alcohol
Secondary amine
Organoheterocyclic compound
Polyol
Azacycle
Primary amine
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:52402 )
ribitol phosphate (CHEBI:52402 )
pyrimidone (CHEBI:52402 )
N-glycosyl compound (CHEBI:52402 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	4.13 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-4.9	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.49	ChemAxon
pKa (Strongest Basic)	6.52	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	232.98 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	84.54 m³·mol⁻¹	ChemAxon
Polarizability	30.98 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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

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
Eukaryota/Fungi	Ascomycota	8	Human feces; Human saliva	Unknown
Bacteria/Eubacteria	Aquificae	1
Archaea/Archaea	Euryarchaeota	3
Archaea	Crenarchaeota	1

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

External Links

HMDB ID

HMDB0304043

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030302

KNApSAcK ID

Not Available

Chemspider ID

23107011

KEGG Compound ID

C18910

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

52402

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone (MMDBc0032981)

MOL for #<Metabolite:0x00005645c9c28188>

3D MOL for #<Metabolite:0x00005645c9c28188>

3D SDF for #<Metabolite:0x00005645c9c28188>

3D-SDF for #<Metabolite:0x00005645c9c28188>

PDB for #<Metabolite:0x00005645c9c28188>

3D PDB for #<Metabolite:0x00005645c9c28188>

SMILES for #<Metabolite:0x00005645c9c28188>

INCHI for #<Metabolite:0x00005645c9c28188>

Structure for #<Metabolite:0x00005645c9c28188>

3D Structure for #<Metabolite:0x00005645c9c28188>