MiMeDB: Showing metabocard for 5'-Phospho-ribosylglycinamide (MMDBc0031737)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:47:08 UTC

Update Date

2022-08-31 18:24:05 UTC

Metabolite ID

MMDBc0031737

Metabolite Identification

Common Name

5'-Phospho-ribosylglycinamide

Description

5-Phospho-ribosylglycinamide is an intermediate in puriine biosynthesis. It is a substrate for the enzyme Phosphoribosylglycinamide synthetase (EC:6.3.4.13) (GARS) which catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'-phosphoribosylglycinamide.

Structure

MOL SDF PDB SMILES InChI

ChEBI
  Mrv0541 02241222352D          

 18 18  0  0  1  0            999 V2000
    7.3235   -9.0935    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.9914   -8.6091    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5779   -9.8784    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.6585   -9.0947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4029   -9.8791    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.4433   -8.8404    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.8873  -10.5469    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0923  -10.5454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5392   -8.8380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5838   -7.7752    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.3683   -8.0308    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7994   -7.5196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8394   -6.9908    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3282   -8.5596    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6016   -8.0537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0595   -7.5666    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.4109   -7.9358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5131   -7.1737    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  6  0  0  0
  3  8  1  6  0  0  0
  1  9  1  1  0  0  0
 11 10  1  0  0  0  0
 12 10  2  0  0  0  0
 13 10  1  0  0  0  0
 14 10  1  0  0  0  0
  9 11  1  0  0  0  0
 15  6  1  0  0  0  0
 16 15  2  0  0  0  0
 17 15  1  0  0  0  0
 18 17  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031737

> <DATABASE_NAME>
MIME

> <SMILES>
NCC(=O)NC1O[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-HJZCUYRDSA-N

> <FORMULA>
C7H15N2O8P

> <MOLECULAR_WEIGHT>
286.1764

> <EXACT_MASS>
286.056601978

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
23.69389940696378

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.40

> <JCHEM_LOGP>
-4.650616976017662

> <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>
55.294799999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.46e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5'-phosphoribosylglycinamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: ChEBI                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      13.671 -16.975   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      14.917 -16.070   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      14.145 -18.440   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.163 -16.977   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      15.685 -18.441   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      17.627 -16.502   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      16.590 -19.688   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      13.239 -19.685   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      12.207 -16.498   0.000  0.00  0.00           C+0
HETATM   10  P   UNK     0      10.423 -14.514   0.000  0.00  0.00           P+0
HETATM   11  O   UNK     0      11.887 -14.991   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       8.959 -14.037   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      10.900 -13.049   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       9.946 -15.978   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      17.923 -15.034   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      16.911 -14.124   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      19.434 -14.813   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      19.624 -13.391   0.000  0.00  0.00           N+0
CONECT    1    2    3    9                                                  
CONECT    2    1    4                                                       
CONECT    3    1    5    8                                                  
CONECT    4    2    5    6                                                  
CONECT    5    3    4    7                                                  
CONECT    6    4   15                                                       
CONECT    7    5                                                            
CONECT    8    3                                                            
CONECT    9    1   11                                                       
CONECT   10   11   12   13   14                                             
CONECT   11   10    9                                                       
CONECT   12   10                                                            
CONECT   13   10                                                            
CONECT   14   10                                                            
CONECT   15    6   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

Synonyms

Value	Source
5'-Phosphoribosylglycinamide	ChEBI
5'-Phosphoribosylglycineamide	ChEBI
GAR	ChEBI
Glycineamide ribonucleotide	ChEBI
Glycineamideribotide	ChEBI
N-Glycyl-5-O-phosphono-D-ribofuranosylamine	ChEBI
N1-(5-Phospho-D-ribosyl)glycinamide	ChEBI
Glycinamide ribonucleotide	ChEBI

Molecular Formula

C₇H₁₅N₂O₈P

Average Mass

286.1764

Monoisotopic Mass

286.056601978

IUPAC Name

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

Traditional Name

5'-phosphoribosylglycinamide

CAS Registry Number

Not Available

SMILES

NCC(=O)NC1O[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-HJZCUYRDSA-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

N-glycosyl compound (CHEBI:18349 )
ribose monophosphate (CHEBI:18349 )

Functional Ontology

Not Available

Physical Properties

State

Expected 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	23.69 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 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

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
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	Activity	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

Not Available

DrugBank ID

DB02236

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5459918

PDB ID

Not Available

ChEBI ID

18349

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Sajed T, Marcu A, Ramirez M, Pon A, Guo AC, Knox C, Wilson M, Grant JR, Djoumbou Y, Wishart DS: ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res. 2016 Jan 4;44(D1):D495-501. doi: 10.1093/nar/gkv1060. Epub 2015 Oct 19. [PubMed:26481353 ]

Showing metabocard for 5'-Phospho-ribosylglycinamide (MMDBc0031737)

MOL for #<Metabolite:0x00007fca48ad9778>

3D MOL for #<Metabolite:0x00007fca48ad9778>

3D SDF for #<Metabolite:0x00007fca48ad9778>

3D-SDF for #<Metabolite:0x00007fca48ad9778>

PDB for #<Metabolite:0x00007fca48ad9778>

3D PDB for #<Metabolite:0x00007fca48ad9778>

SMILES for #<Metabolite:0x00007fca48ad9778>

INCHI for #<Metabolite:0x00007fca48ad9778>

Structure for #<Metabolite:0x00007fca48ad9778>

3D Structure for #<Metabolite:0x00007fca48ad9778>