MiMeDB: Showing metabocard for 2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone (MMDBc0029988)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:49:35 UTC

Update Date

2022-08-31 17:38:24 UTC

Metabolite ID

MMDBc0029988

Metabolite Identification

Common Name

2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone

Description

2,5-diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone is a nucleotide analog. It is involved in cofactor biosynthesis and riboflavin biosynthesis

Structure

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

HMDB0304044
     RDKit          3D
2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one
 39 40  0  0  0  0  0  0  0  0999 V2000
   -5.1906   -0.9393   -0.1326 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1539    0.0153   -0.3676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9277   -0.1150    0.1512 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9156    0.7676   -0.0470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6587    0.5553    0.5345 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -0.5563    1.3648 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0135   -0.5109    1.8005 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7987   -1.2413    0.9543 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7704   -0.3797    0.1686 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6017    0.2916    1.0657 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7143    1.2724    0.2966 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.7641    1.7168    1.2827 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5349    0.4005   -0.9209 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9393    2.5955   -0.4372 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9132   -1.9491   -0.0272 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2555   -3.3071   -0.0822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4194   -1.8878    0.7306 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5248   -2.9429    1.5966 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1516    1.8747   -0.8314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1452    2.8559   -1.0938 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4164    2.0061   -1.3646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6198    3.0315   -2.0857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3833    1.0999   -1.1354 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1899   -0.6880    0.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9523   -1.9537   -0.1154 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0970    1.2630    0.3560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9350   -0.5616    2.2946 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3804   -1.9662    1.5921 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2020    0.3917   -0.3889 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3295   -0.9650   -0.5678 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1390   -0.2738   -0.5225 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6104    3.3243   -0.5908 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8446   -1.4884   -1.0084 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0122   -3.7748    0.7444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2000   -1.9647   -0.0481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9883   -3.6843    1.1315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7996    3.0370   -2.0644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7142    3.4301   -0.3370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3325    1.2207   -1.5496 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
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  8 15  1  0
 15 16  1  0
 15 17  1  0
 17 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
 17  6  1  0
  1 24  1  0
  1 25  1  0
  5 26  1  0
  6 27  1  1
  8 28  1  1
  9 29  1  0
  9 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  6
 16 34  1  0
 17 35  1  6
 18 36  1  0
 20 37  1  0
 20 38  1  0
 23 39  1  0
M  END


  Mrv1652303082006172D          

 23 24  0  0  0  0            999 V2000
   -0.7260    3.6627    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7260    2.8377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0115    2.4252    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0115    1.6002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7029    1.1877    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7029    0.3627    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0354   -0.1221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2904   -0.9067    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1945   -1.5742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1410   -2.3278    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3438   -2.9953    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8287   -3.6627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3235   -3.4802    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0113   -2.5104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1154   -0.9067    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6003   -1.5742    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3703   -0.1221    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1549    0.1327    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7260    1.1877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7260    0.3627    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4405    1.6002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1549    1.1877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4405    2.4252    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 11 14  2  0  0  0  0
  8 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
  6 17  1  0  0  0  0
 17 18  1  6  0  0  0
  4 19  2  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
  2 23  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029988

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC(N[C@@H]2O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]2O)=C(N)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C9H16N5O8P/c10-3-6(13-9(11)14-7(3)17)12-8-5(16)4(15)2(22-8)1-21-23(18,19)20/h2,4-5,8,15-16H,1,10H2,(H2,18,19,20)(H4,11,12,13,14,17)/t2-,4-,5-,8-/m1/s1

> <INCHI_KEY>
OCLCLRXKNJCOJD-UMMCILCDSA-N

> <FORMULA>
C9H16N5O8P

> <MOLECULAR_WEIGHT>
353.2258

> <EXACT_MASS>
353.073649025

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
29.99048991004865

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.25

> <JCHEM_LOGP>
-4.229207798436231

> <ALOGPS_LOGS>
-1.79

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.240036904309666

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.052770410004614

> <JCHEM_PKA_STRONGEST_BASIC>
1.7093533470768942

> <JCHEM_POLAR_SURFACE_AREA>
221.98

> <JCHEM_REFRACTIVITY>
82.05649999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.70e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
APy

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0304044
     RDKit          3D
2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one
 39 40  0  0  0  0  0  0  0  0999 V2000
   -5.1906   -0.9393   -0.1326 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1539    0.0153   -0.3676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9277   -0.1150    0.1512 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9156    0.7676   -0.0470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6587    0.5553    0.5345 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -0.5563    1.3648 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0135   -0.5109    1.8005 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7987   -1.2413    0.9543 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7704   -0.3797    0.1686 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6017    0.2916    1.0657 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7143    1.2724    0.2966 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.7641    1.7168    1.2827 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5349    0.4005   -0.9209 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9393    2.5955   -0.4372 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9132   -1.9491   -0.0272 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2555   -3.3071   -0.0822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4194   -1.8878    0.7306 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5248   -2.9429    1.5966 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1516    1.8747   -0.8314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1452    2.8559   -1.0938 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4164    2.0061   -1.3646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6198    3.0315   -2.0857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3833    1.0999   -1.1354 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1899   -0.6880    0.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9523   -1.9537   -0.1154 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0970    1.2630    0.3560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9350   -0.5616    2.2946 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3804   -1.9662    1.5921 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2020    0.3917   -0.3889 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3295   -0.9650   -0.5678 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1390   -0.2738   -0.5225 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6104    3.3243   -0.5908 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8446   -1.4884   -1.0084 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0122   -3.7748    0.7444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2000   -1.9647   -0.0481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9883   -3.6843    1.1315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7996    3.0370   -2.0644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7142    3.4301   -0.3370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3325    1.2207   -1.5496 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
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  8 15  1  0
 15 16  1  0
 15 17  1  0
 17 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
 17  6  1  0
  1 24  1  0
  1 25  1  0
  5 26  1  0
  6 27  1  1
  8 28  1  1
  9 29  1  0
  9 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  6
 16 34  1  0
 17 35  1  6
 18 36  1  0
 20 37  1  0
 20 38  1  0
 23 39  1  0
M  END

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  N   UNK     0      -1.355   6.837   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -1.355   5.297   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -0.021   4.527   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -0.021   2.987   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.312   2.217   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.312   0.677   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.066  -0.228   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.542  -1.693   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.363  -2.939   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.263  -4.345   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0      -0.642  -5.591   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      -1.547  -6.837   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.604  -6.496   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.888  -4.686   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.082  -1.693   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.987  -2.939   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.558  -0.228   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.022   0.248   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -1.355   2.217   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0      -1.355   0.677   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      -2.689   2.987   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -4.022   2.217   0.000  0.00  0.00           O+0
HETATM   23  N   UNK     0      -2.689   4.527   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   23                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   19                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   17                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   15                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
CONECT   15    8   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    6   18                                                  
CONECT   18   17                                                            
CONECT   19    4   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21    2                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

COMPND    HMDB0304044
HETATM    1  N1  UNL     1      -5.191  -0.939  -0.133  1.00  0.00           N  
HETATM    2  C1  UNL     1      -4.154   0.015  -0.368  1.00  0.00           C  
HETATM    3  N2  UNL     1      -2.928  -0.115   0.151  1.00  0.00           N  
HETATM    4  C2  UNL     1      -1.916   0.768  -0.047  1.00  0.00           C  
HETATM    5  N3  UNL     1      -0.659   0.555   0.534  1.00  0.00           N  
HETATM    6  C3  UNL     1      -0.302  -0.556   1.365  1.00  0.00           C  
HETATM    7  O1  UNL     1       1.013  -0.511   1.801  1.00  0.00           O  
HETATM    8  C4  UNL     1       1.799  -1.241   0.954  1.00  0.00           C  
HETATM    9  C5  UNL     1       2.770  -0.380   0.169  1.00  0.00           C  
HETATM   10  O2  UNL     1       3.602   0.292   1.066  1.00  0.00           O  
HETATM   11  P1  UNL     1       4.714   1.272   0.297  1.00  0.00           P  
HETATM   12  O3  UNL     1       5.764   1.717   1.283  1.00  0.00           O  
HETATM   13  O4  UNL     1       5.535   0.401  -0.921  1.00  0.00           O  
HETATM   14  O5  UNL     1       3.939   2.596  -0.437  1.00  0.00           O  
HETATM   15  C6  UNL     1       0.913  -1.949  -0.027  1.00  0.00           C  
HETATM   16  O6  UNL     1       1.256  -3.307  -0.082  1.00  0.00           O  
HETATM   17  C7  UNL     1      -0.419  -1.888   0.731  1.00  0.00           C  
HETATM   18  O7  UNL     1      -0.525  -2.943   1.597  1.00  0.00           O  
HETATM   19  C8  UNL     1      -2.152   1.875  -0.831  1.00  0.00           C  
HETATM   20  N4  UNL     1      -1.145   2.856  -1.094  1.00  0.00           N  
HETATM   21  C9  UNL     1      -3.416   2.006  -1.365  1.00  0.00           C  
HETATM   22  O8  UNL     1      -3.620   3.032  -2.086  1.00  0.00           O  
HETATM   23  N5  UNL     1      -4.383   1.100  -1.135  1.00  0.00           N  
HETATM   24  H1  UNL     1      -6.190  -0.688   0.026  1.00  0.00           H  
HETATM   25  H2  UNL     1      -4.952  -1.954  -0.115  1.00  0.00           H  
HETATM   26  H3  UNL     1       0.097   1.263   0.356  1.00  0.00           H  
HETATM   27  H4  UNL     1      -0.935  -0.562   2.295  1.00  0.00           H  
HETATM   28  H5  UNL     1       2.380  -1.966   1.592  1.00  0.00           H  
HETATM   29  H6  UNL     1       2.202   0.392  -0.389  1.00  0.00           H  
HETATM   30  H7  UNL     1       3.329  -0.965  -0.568  1.00  0.00           H  
HETATM   31  H8  UNL     1       6.139  -0.274  -0.522  1.00  0.00           H  
HETATM   32  H9  UNL     1       4.610   3.324  -0.591  1.00  0.00           H  
HETATM   33  H10 UNL     1       0.845  -1.488  -1.008  1.00  0.00           H  
HETATM   34  H11 UNL     1       1.012  -3.775   0.744  1.00  0.00           H  
HETATM   35  H12 UNL     1      -1.200  -1.965  -0.048  1.00  0.00           H  
HETATM   36  H13 UNL     1      -0.988  -3.684   1.132  1.00  0.00           H  
HETATM   37  H14 UNL     1      -0.800   3.037  -2.064  1.00  0.00           H  
HETATM   38  H15 UNL     1      -0.714   3.430  -0.337  1.00  0.00           H  
HETATM   39  H16 UNL     1      -5.333   1.221  -1.550  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   17   27
CONECT    7    8
CONECT    8    9   15   28
CONECT    9   10   29   30
CONECT   10   11
CONECT   11   12   12   13   14
CONECT   13   31
CONECT   14   32
CONECT   15   16   17   33
CONECT   16   34
CONECT   17   18   35
CONECT   18   36
CONECT   19   20   21
CONECT   20   37   38
CONECT   21   22   22   23
CONECT   23   39
END

HMDB0304044
     RDKit          3D
2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one
 39 40  0  0  0  0  0  0  0  0999 V2000
   -5.1906   -0.9393   -0.1326 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1539    0.0153   -0.3676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9277   -0.1150    0.1512 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9156    0.7676   -0.0470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6587    0.5553    0.5345 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -0.5563    1.3648 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0135   -0.5109    1.8005 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7987   -1.2413    0.9543 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7704   -0.3797    0.1686 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6017    0.2916    1.0657 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7143    1.2724    0.2966 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.7641    1.7168    1.2827 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5349    0.4005   -0.9209 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9393    2.5955   -0.4372 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9132   -1.9491   -0.0272 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2555   -3.3071   -0.0822 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4194   -1.8878    0.7306 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5248   -2.9429    1.5966 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1516    1.8747   -0.8314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1452    2.8559   -1.0938 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4164    2.0061   -1.3646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6198    3.0315   -2.0857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3833    1.0999   -1.1354 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1899   -0.6880    0.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9523   -1.9537   -0.1154 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0970    1.2630    0.3560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9350   -0.5616    2.2946 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3804   -1.9662    1.5921 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2020    0.3917   -0.3889 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3295   -0.9650   -0.5678 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1390   -0.2738   -0.5225 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6104    3.3243   -0.5908 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8446   -1.4884   -1.0084 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0122   -3.7748    0.7444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2000   -1.9647   -0.0481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9883   -3.6843    1.1315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7996    3.0370   -2.0644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7142    3.4301   -0.3370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3325    1.2207   -1.5496 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
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 11 14  1  0
  8 15  1  0
 15 16  1  0
 15 17  1  0
 17 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
 17  6  1  0
  1 24  1  0
  1 25  1  0
  5 26  1  0
  6 27  1  1
  8 28  1  1
  9 29  1  0
  9 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  6
 16 34  1  0
 17 35  1  6
 18 36  1  0
 20 37  1  0
 20 38  1  0
 23 39  1  0
M  END

Synonyms

Value	Source
2,5-Diamino-6-hydroxy-4-(5'-phosphoribosylamino)-pyrimidine	ChEBI
2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine	ChEBI
N-(2,5-Diamino-6-hydroxypyrimidin-4-yl)-5-O-phosphono-beta-D-ribofuranosylamine	ChEBI
2,5-Diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate	Kegg
N-(2,5-Diamino-6-hydroxypyrimidin-4-yl)-5-O-phosphono-b-D-ribofuranosylamine	Generator
N-(2,5-Diamino-6-hydroxypyrimidin-4-yl)-5-O-phosphono-β-D-ribofuranosylamine	Generator
2,5-Diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphoric acid	Generator

Molecular Formula

C₉H₁₆N₅O₈P

Average Mass

353.2258

Monoisotopic Mass

353.073649025

IUPAC Name

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

Traditional Name

APy

CAS Registry Number

Not Available

SMILES

NC1=NC(N[C@@H]2O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]2O)=C(N)C(=O)N1

InChI Identifier

InChI=1S/C9H16N5O8P/c10-3-6(13-9(11)14-7(3)17)12-8-5(16)4(15)2(22-8)1-21-23(18,19)20/h2,4-5,8,15-16H,1,10H2,(H2,18,19,20)(H4,11,12,13,14,17)/t2-,4-,5-,8-/m1/s1

InChI Key

OCLCLRXKNJCOJD-UMMCILCDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Aminopyrimidine
Pyrimidone
Secondary aliphatic/aromatic amine
Monoalkyl phosphate
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Hydropyrimidine
Organic phosphoric acid derivative
Tetrahydrofuran
Heteroaromatic compound
Vinylogous amide
1,2-diol
Secondary alcohol
Secondary amine
Oxacycle
Azacycle
Organoheterocyclic compound
Amine
Organic oxide
Organonitrogen compound
Organopnictogen compound
Organic nitrogen compound
Hydrocarbon derivative
Primary amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

hydroxypyrimidine (CHEBI:29114 )
aminopyrimidine (CHEBI:29114 )
N-glycosyl compound (CHEBI:29114 )
ribose monophosphate (CHEBI:29114 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	5.7 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-4.2	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	1.05	ChemAxon
pKa (Strongest Basic)	1.71	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	221.98 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	82.06 m³·mol⁻¹	ChemAxon
Polarizability	29.99 Å³	ChemAxon
Number of Rings	2	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
MMDBr0019042	Guanosine triphosphate	Formic acid	GTP cyclohydrolase 1	Hydrolysis of bond	PathBank	31602464
MMDBr0019046	2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone	5-Amino-6-(5'-phosphoribosylamino)uracil	Riboflavin biosynthesis protein RibD	Synthesis	PathBank	31602464

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	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
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

External Links

HMDB ID

HMDB0304044

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030303

KNApSAcK ID

Not Available

Chemspider ID

388579

KEGG Compound ID

C01304

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

29114

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for 2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone (MMDBc0029988)

MOL for #<Metabolite:0x00007f92352af458>

3D MOL for #<Metabolite:0x00007f92352af458>

3D SDF for #<Metabolite:0x00007f92352af458>

3D-SDF for #<Metabolite:0x00007f92352af458>

PDB for #<Metabolite:0x00007f92352af458>

3D PDB for #<Metabolite:0x00007f92352af458>

SMILES for #<Metabolite:0x00007f92352af458>

INCHI for #<Metabolite:0x00007f92352af458>

Structure for #<Metabolite:0x00007f92352af458>

3D Structure for #<Metabolite:0x00007f92352af458>