P. aeruginosa Metabolome Database: Glycineamideribotide (PAMDB000422)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB000422

Identification

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.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

5'-p-Ribosylglycinamide
5'-p-Ribosylglycineamide
5'-Phosphoribosyl-glycineamide
5'-Phosphoribosylglycinamide
5'-Phosphoribosylglycineamide
GAR
Glycinamide ribonucleotide
Glycineamide ribonucleotide
N(1)-(5-Phospho-D-ribosyl)glycinamide
N-Glycyl-5-O-phosphono-D-ribofuranosylamine
N1-(5-phospho-D-ribosyl)glycinamide

Chemical Formula:

C₇H₁₅N₂O₈P

Average Molecular Weight:

286.1764

Monoisotopic Molecular Weight:

286.056601978

InChI Key:

OBQMLSFOUZUIOB-SHUUEZRQSA-N

InChI:

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

CAS number:

10074-18-7

IUPAC Name:

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

Traditional IUPAC Name:

glycineamide ribonucleotide

SMILES:

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

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of organic compounds known as glycinamide ribonucleotides. These 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
Alpha-amino acid amide
Monosaccharide phosphate
Alpha-amino acid or derivatives
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Organic phosphate
Monosaccharide
Saccharide
Oxolane
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
1,2-diol
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Carboxylic acid amide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Solid

Charge:

-1

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	14.6 mg/mL	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	23.71 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

Pathways:

Metabolic pathways pae01100
One carbon pool by folate pae00670
Purine metabolism pae00230

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-MS	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-053i-9460000000-f71dc4d8ec0f4da03819	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0560-9120000000-4770933b45387be6728c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a59-9200000000-a6f2b9ab201fd0e69ee8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0170-9550000000-99520656892b8c415efb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-d6c860661b01956c80ac	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-c2f2b85e6ec9caaa4408	View in MoNA

References

References:

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. Pubmed: 9143358
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
McKerns KW: Gonadotropin regulation of nucleotide biosynthesis in corpus luteum. Biochemistry. 1973 Dec 4;12(25):5206-11. Pubmed: 4366083

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	18349
HMDB ID	HMDB02022
Pubchem Compound ID	440137
Kegg ID	C03838
ChemSpider ID	141370
Wikipedia ID	Glycineamide ribonucleotide
BioCyc ID	5-PHOSPHO-RIBOSYL-GLYCINEAMIDE
EcoCyc ID	5-PHOSPHO-RIBOSYL-GLYCINEAMIDE
Ligand Expo	GAR

Glycineamideribotide (PAMDB000422)

Structure for Glycineamideribotide (PAMDB000422)