MiMeDB: Showing metabocard for Glycineamideribotide (MMDBc0029672)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:36:56 UTC

Update Date

2024-04-30 19:40:26 UTC

Metabolite ID

MMDBc0029672

Metabolite Identification

Common Name

Glycineamideribotide

Description

Glycinamidoribotide conversion to N-formylglycinamide ribonucleotide is the third reaction of the de novo purine biosynthesis, a reaction catalyzed by the enzyme glycinamide ribonucleotide transformylase (EC 2.1.2.2). Glycinamide ribonucleotide (GAR) synthetase catalyzes the conversion of phosphoribosylamine, glycine, and MgATP to glycinamide ribonucleotide. (PMID: 2182115 )

Structure

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

HMDB0002022
     RDKit          3D
Glycineamideribotide
 33 33  0  0  0  0  0  0  0  0999 V2000
   -5.1914   -2.8560    0.0864 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5905   -1.5615   -0.1750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1126   -1.6876   -0.1449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5539   -2.7907    0.0811 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2806   -0.5615   -0.3714 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8416   -0.6537   -0.3483 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2688    0.2002    0.6014 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0848    0.1094    0.2505 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9317    1.0844    1.0167 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2497    0.9125    0.5953 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3100    1.9661    1.3949 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.6315    1.9523    0.6768 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5665    1.3751    2.9588 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6168    3.4920    1.4666 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0257    0.5345   -1.2100 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1039    0.0538   -1.9386 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2870   -0.1075   -1.6385 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0497   -1.1546   -2.5386 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2033   -2.8258   -0.1502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0239   -3.0577    1.1093 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9193   -1.1240   -1.1413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9532   -0.8827    0.6435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7260    0.3656   -0.5612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4908   -1.6686   -0.1409 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4846   -0.9016    0.3656 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8942    0.8757    2.1000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6239    2.1332    0.8190 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1406    0.4914    3.0823 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9691    4.0624    2.1828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9538    1.6431   -1.2454 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8342    0.7146   -1.9520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9495    0.6603   -2.0647 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0212   -0.7928   -3.4614 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  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
 17  6  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  2 22  1  0
  5 23  1  0
  6 24  1  1
  8 25  1  6
  9 26  1  0
  9 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  1
 16 31  1  0
 17 32  1  6
 18 33  1  0
M  END


  Mrv1652306232018152D          

 18 18  0  0  0  0            999 V2000
10001.391910000.5628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.106710000.1508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.819410000.5628    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10002.409510001.2755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.534210000.1508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.233410001.2755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.8852 9998.7044    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.627810000.5628    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9999.0941 9998.7126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.913810000.1508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.199910000.5628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.9138 9999.3263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.485710000.1508    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10000.006310000.6450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.338910000.1600    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.5938 9999.3754    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.4188 9999.3754    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.673710000.1600    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
 11 13  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 14 15  1  0  0  0  0
 14 18  1  0  0  0  0
 18  1  1  6  0  0  0
 17  7  1  1  0  0  0
 15  8  1  6  0  0  0
 16  9  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029672

> <DATABASE_NAME>
MIME

> <SMILES>
NCC(=O)N[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/t3-,5-,6-,7-/m1/s1

> <INCHI_KEY>
OBQMLSFOUZUIOB-SHUUEZRQSA-N

> <FORMULA>
C7H15N2O8P

> <MOLECULAR_WEIGHT>
286.1764

> <EXACT_MASS>
286.056601978

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
23.677380162378174

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-(2-aminoacetamido)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-2.40

> <JCHEM_LOGP>
-4.650616976017661

> <ALOGPS_LOGS>
-1.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.245768050847792

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2255744528280514

> <JCHEM_PKA_STRONGEST_BASIC>
8.141960108603826

> <JCHEM_POLAR_SURFACE_AREA>
171.57000000000002

> <JCHEM_REFRACTIVITY>
55.2948

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.46e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glycineamide ribonucleotide

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0002022
     RDKit          3D
Glycineamideribotide
 33 33  0  0  0  0  0  0  0  0999 V2000
   -5.1914   -2.8560    0.0864 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5905   -1.5615   -0.1750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1126   -1.6876   -0.1449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5539   -2.7907    0.0811 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2806   -0.5615   -0.3714 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8416   -0.6537   -0.3483 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2688    0.2002    0.6014 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0848    0.1094    0.2505 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9317    1.0844    1.0167 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2497    0.9125    0.5953 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3100    1.9661    1.3949 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.6315    1.9523    0.6768 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5665    1.3751    2.9588 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6168    3.4920    1.4666 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0257    0.5345   -1.2100 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1039    0.0538   -1.9386 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2870   -0.1075   -1.6385 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0497   -1.1546   -2.5386 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2033   -2.8258   -0.1502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0239   -3.0577    1.1093 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9193   -1.1240   -1.1413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9532   -0.8827    0.6435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7260    0.3656   -0.5612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4908   -1.6686   -0.1409 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4846   -0.9016    0.3656 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8942    0.8757    2.1000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6239    2.1332    0.8190 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1406    0.4914    3.0823 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9691    4.0624    2.1828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9538    1.6431   -1.2454 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8342    0.7146   -1.9520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9495    0.6603   -2.0647 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0212   -0.7928   -3.4614 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  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
 17  6  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  2 22  1  0
  5 23  1  0
  6 24  1  1
  8 25  1  6
  9 26  1  0
  9 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  1
 16 31  1  0
 17 32  1  6
 18 33  1  0
M  END

HEADER    PROTEIN                                 23-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-JUN-20         0                                  
HETATM    1  C   UNK     0    8669.2658667.717   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8670.5998666.948   0.000  0.00  0.00           O+0
HETATM    3  P   UNK     0    8671.9308667.717   0.000  0.00  0.00           P+0
HETATM    4  O   UNK     0    8671.1648669.048   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8673.2648666.948   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8672.7028669.048   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8668.3198664.248   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0    8664.1058667.717   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0    8664.9768664.264   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0    8662.7728666.948   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8661.4408667.717   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0    8662.7728665.409   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0    8660.1078666.948   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0    8666.6788667.871   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0    8665.4338666.965   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8665.9088665.501   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8667.4488665.501   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8667.9248666.965   0.000  0.00  0.00           C+0
CONECT    1    2   18                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3                                                            
CONECT    7   17                                                            
CONECT    8   10   15                                                       
CONECT    9   16                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10   13                                                       
CONECT   12   10                                                            
CONECT   13   11                                                            
CONECT   14   15   18                                                       
CONECT   15   16   14    8                                                  
CONECT   16   15   17    9                                                  
CONECT   17   16   18    7                                                  
CONECT   18   17   14    1                                                  
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

COMPND    HMDB0002022
HETATM    1  N1  UNL     1      -5.191  -2.856   0.086  1.00  0.00           N  
HETATM    2  C1  UNL     1      -4.591  -1.562  -0.175  1.00  0.00           C  
HETATM    3  C2  UNL     1      -3.113  -1.688  -0.145  1.00  0.00           C  
HETATM    4  O1  UNL     1      -2.554  -2.791   0.081  1.00  0.00           O  
HETATM    5  N2  UNL     1      -2.281  -0.561  -0.371  1.00  0.00           N  
HETATM    6  C3  UNL     1      -0.842  -0.654  -0.348  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.269   0.200   0.601  1.00  0.00           O  
HETATM    8  C4  UNL     1       1.085   0.109   0.251  1.00  0.00           C  
HETATM    9  C5  UNL     1       1.932   1.084   1.017  1.00  0.00           C  
HETATM   10  O3  UNL     1       3.250   0.912   0.595  1.00  0.00           O  
HETATM   11  P1  UNL     1       4.310   1.966   1.395  1.00  0.00           P  
HETATM   12  O4  UNL     1       5.631   1.952   0.677  1.00  0.00           O  
HETATM   13  O5  UNL     1       4.567   1.375   2.959  1.00  0.00           O  
HETATM   14  O6  UNL     1       3.617   3.492   1.467  1.00  0.00           O  
HETATM   15  C6  UNL     1       1.026   0.534  -1.210  1.00  0.00           C  
HETATM   16  O7  UNL     1       2.104   0.054  -1.939  1.00  0.00           O  
HETATM   17  C7  UNL     1      -0.287  -0.107  -1.639  1.00  0.00           C  
HETATM   18  O8  UNL     1      -0.050  -1.155  -2.539  1.00  0.00           O  
HETATM   19  H1  UNL     1      -6.203  -2.826  -0.150  1.00  0.00           H  
HETATM   20  H2  UNL     1      -5.024  -3.058   1.109  1.00  0.00           H  
HETATM   21  H3  UNL     1      -4.919  -1.124  -1.141  1.00  0.00           H  
HETATM   22  H4  UNL     1      -4.953  -0.883   0.643  1.00  0.00           H  
HETATM   23  H5  UNL     1      -2.726   0.366  -0.561  1.00  0.00           H  
HETATM   24  H6  UNL     1      -0.491  -1.669  -0.141  1.00  0.00           H  
HETATM   25  H7  UNL     1       1.485  -0.902   0.366  1.00  0.00           H  
HETATM   26  H8  UNL     1       1.894   0.876   2.100  1.00  0.00           H  
HETATM   27  H9  UNL     1       1.624   2.133   0.819  1.00  0.00           H  
HETATM   28  H10 UNL     1       4.141   0.491   3.082  1.00  0.00           H  
HETATM   29  H11 UNL     1       3.969   4.062   2.183  1.00  0.00           H  
HETATM   30  H12 UNL     1       0.954   1.643  -1.245  1.00  0.00           H  
HETATM   31  H13 UNL     1       2.834   0.715  -1.952  1.00  0.00           H  
HETATM   32  H14 UNL     1      -0.949   0.660  -2.065  1.00  0.00           H  
HETATM   33  H15 UNL     1       0.021  -0.793  -3.461  1.00  0.00           H  
CONECT    1    2   19   20
CONECT    2    3   21   22
CONECT    3    4    4    5
CONECT    5    6   23
CONECT    6    7   17   24
CONECT    7    8
CONECT    8    9   15   25
CONECT    9   10   26   27
CONECT   10   11
CONECT   11   12   12   13   14
CONECT   13   28
CONECT   14   29
CONECT   15   16   17   30
CONECT   16   31
CONECT   17   18   32
CONECT   18   33
END

HMDB0002022
     RDKit          3D
Glycineamideribotide
 33 33  0  0  0  0  0  0  0  0999 V2000
   -5.1914   -2.8560    0.0864 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5905   -1.5615   -0.1750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1126   -1.6876   -0.1449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5539   -2.7907    0.0811 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2806   -0.5615   -0.3714 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8416   -0.6537   -0.3483 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2688    0.2002    0.6014 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0848    0.1094    0.2505 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9317    1.0844    1.0167 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2497    0.9125    0.5953 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3100    1.9661    1.3949 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.6315    1.9523    0.6768 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5665    1.3751    2.9588 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6168    3.4920    1.4666 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0257    0.5345   -1.2100 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1039    0.0538   -1.9386 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2870   -0.1075   -1.6385 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0497   -1.1546   -2.5386 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2033   -2.8258   -0.1502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0239   -3.0577    1.1093 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9193   -1.1240   -1.1413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9532   -0.8827    0.6435 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7260    0.3656   -0.5612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4908   -1.6686   -0.1409 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4846   -0.9016    0.3656 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8942    0.8757    2.1000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6239    2.1332    0.8190 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1406    0.4914    3.0823 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9691    4.0624    2.1828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9538    1.6431   -1.2454 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8342    0.7146   -1.9520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9495    0.6603   -2.0647 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0212   -0.7928   -3.4614 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  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
 17  6  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  2 22  1  0
  5 23  1  0
  6 24  1  1
  8 25  1  6
  9 26  1  0
  9 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  1
 16 31  1  0
 17 32  1  6
 18 33  1  0
M  END

Synonyms

Value	Source
GAR	Kegg
N1-(5-Phospho-D-ribosyl)glycinamide	Kegg
Glycinamide ribonucleotide	Kegg
N1-(5-Phospho-beta-D-ribosyl)glycinamide	Kegg
N1-(5-Phospho-b-D-ribosyl)glycinamide	Generator
N1-(5-Phospho-β-D-ribosyl)glycinamide	Generator
5'-Phosphoribosyl-glycineamide	HMDB
5'-Phosphoribosylglycinamide	HMDB
5'-Phosphoribosylglycineamide	HMDB
Glycineamide ribonucleotide	HMDB
N(1)-(5-phospho-D-Ribosyl)glycinamide	HMDB
N-Glycyl-5-O-phosphono-D-ribofuranosylamine	HMDB
2-Amino-N-(5-O-phosphono-beta-D-ribofuranosyl)acetamide	HMDB
2-Amino-N-(5-O-phosphono-β-D-ribofuranosyl)acetamide	HMDB
5-Phospho-beta-D-ribosyl-glycineamide	HMDB
5-Phospho-β-D-ribosyl-glycineamide	HMDB
5’-Phosphoribosylglycinamide	HMDB
5’-Phosphoribosylglycineamide	HMDB

Molecular Formula

C₇H₁₅N₂O₈P

Average Mass

286.1764

Monoisotopic Mass

286.056601978

IUPAC Name

{[(2R,3S,4R,5R)-5-(2-aminoacetamido)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

glycineamide ribonucleotide

CAS Registry Number

10074-18-7

SMILES

NCC(=O)N[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/t3-,5-,6-,7-/m1/s1

InChI Key

OBQMLSFOUZUIOB-SHUUEZRQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycinamide ribonucleotides. Glycinamide ribonucleotides are compounds in which the amide N atom of glycineamide is linked to the C-1 of a ribosyl (or deoxyribosyl) moiety. Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Glycinamide ribonucleotides

Sub Class

Not Available

Direct Parent

Glycinamide ribonucleotides

Alternative Parents

Substituents

Glycinamide-ribonucleotide
Pentose phosphate
Pentose-5-phosphate
Alpha-amino acid amide
Alpha-amino acid or derivatives
Monosaccharide phosphate
Pentose monosaccharide
Monoalkyl phosphate
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Tetrahydrofuran
Secondary carboxylic acid amide
Secondary alcohol
Amino acid or derivatives
Carboxamide group
1,2-diol
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Organic nitrogen compound
Organic oxide
Primary aliphatic amine
Organopnictogen compound
Alcohol
Organonitrogen compound
Carbonyl group
Organooxygen compound
Amine
Organic oxygen compound
Hydrocarbon derivative
Primary amine
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	14.6 g/L	ALOGPS
logP	-2.4	ALOGPS
logP	-4.7	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	8.14	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	171.57 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	55.29 m³·mol⁻¹	ChemAxon
Polarizability	23.68 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-000t-9420000000-d7fee78dd4657e2eba28	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00si-9541200000-4a23e3091baf72b01dc2	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-053i-9460000000-f71dc4d8ec0f4da03819	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0560-9120000000-4770933b45387be6728c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a59-9200000000-a6f2b9ab201fd0e69ee8	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0170-9550000000-99520656892b8c415efb	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-d6c860661b01956c80ac	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-c2f2b85e6ec9caaa4408	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-2090000000-f6fcd99577c7e5d5d2ec	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9020000000-f5f361d4aef59382fc15	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-962cd48ee45a1c95e446	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0980000000-6a9e014a86b77c5ad3c3	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-5920000000-cb0c5e3520ad275d3742	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-057j-9500000000-ab2ea8c5eb8a25044810	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

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
MMDBp0191999	Trifunctional purine biosynthetic protein adenosine-3	Enzyme	P22102	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0001270	10-Formyltetrahydrofolic acid	5'-Phosphoribosyl-N-formylglycineamide	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	VMH; KEGG	12450384 2183217 9328467 9473452
MMDBr0001986	Glycine	Glycineamideribotide	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	VMH; KEGG	30371894
MMDBr0006939	10-Formyltetrahydrofolic acid	5'-Phosphoribosyl-N-formylglycineamide	Not Available	VMH	30371894
MMDBr0007063	Formic acid	5'-Phosphoribosyl-N-formylglycineamide	Not Available	VMH	30371894
MMDBr0007542	Glycine	Glycineamideribotide	Not Available	VMH	30371894

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	Proteobacteria	182	Human feces; Human sputum; Human ; 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	Firmicutes	383	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	126	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	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	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

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

HMDB0002022

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

5-PHOSPHO-RIBOSYL-GLYCINEAMIDE

BiGG ID

42621

Wikipedia Link

Glycineamide ribonucleotide

METLIN ID

Not Available

PubChem Compound

160913

PDB ID

Not Available

ChEBI ID

18349

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

McKerns KW: Gonadotropin regulation of nucleotide biosynthesis in corpus luteum. Biochemistry. 1973 Dec 4;12(25):5206-11. doi: 10.1021/bi00749a030. [PubMed:4366083 ]
Caperelli CA, Giroux EL: The human glycinamide ribonucleotide transformylase domain: purification, characterization, and kinetic mechanism. Arch Biochem Biophys. 1997 May 1;341(1):98-103. doi: 10.1006/abbi.1997.9947. [PubMed:9143358 ]

Showing metabocard for Glycineamideribotide (MMDBc0029672)

MOL for #<Metabolite:0x00007fdb30a9c208>

3D MOL for #<Metabolite:0x00007fdb30a9c208>

3D SDF for #<Metabolite:0x00007fdb30a9c208>

3D-SDF for #<Metabolite:0x00007fdb30a9c208>

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Structure for #<Metabolite:0x00007fdb30a9c208>

3D Structure for #<Metabolite:0x00007fdb30a9c208>