MiMeDB: Showing metabocard for N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide (MMDBc0033116)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:35:27 UTC

Update Date

2022-08-31 22:26:21 UTC

Metabolite ID

MMDBc0033116

Metabolite Identification

Common Name

N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide

Description

Structure

MOL SDF PDB SMILES InChI

ChEBI
  Mrv0541 02241222352D          

 20 20  0  0  1  0            999 V2000
   15.1153   -8.5658    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.9403   -8.5658    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.7028   -9.2803    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3528   -9.2803    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.8604   -7.7813    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.1459   -7.3688    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4314   -7.7813    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6064   -6.9563    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.7814   -7.7813    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6064   -7.7813    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   12.6064   -8.6063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5278   -7.2963    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.1952   -7.7813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9097   -7.3688    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.6242   -8.6063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.6242   -7.7813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.3386   -7.3688    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.0531   -7.7813    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.7676   -7.3688    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.4820   -7.7813    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 12  5  1  0  0  0  0
 12 13  1  0  0  0  0
  5  1  1  0  0  0  0
  1  2  1  0  0  0  0
  2 13  1  0  0  0  0
  1  3  1  6  0  0  0
  2  4  1  6  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7 10  1  0  0  0  0
 10  8  2  0  0  0  0
 10  9  1  0  0  0  0
 10 11  1  0  0  0  0
 13 14  1  0  0  0  0
 14 16  1  0  0  0  0
 16 15  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033116

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@H]1[C@@H](O)C(NC(=O)CNC=O)O[C@@H]1COP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H15N2O9P/c11-3-9-1-5(12)10-8-7(14)6(13)4(19-8)2-18-20(15,16)17/h3-4,6-8,13-14H,1-2H2,(H,9,11)(H,10,12)(H2,15,16,17)/t4-,6-,7-,8?/m1/s1

> <INCHI_KEY>
VDXLUNDMVKSKHO-ZRTZXPPTSA-N

> <FORMULA>
C8H15N2O9P

> <MOLECULAR_WEIGHT>
314.1865

> <EXACT_MASS>
314.0515166

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
25.664654078934777

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.28

> <JCHEM_LOGP>
-3.8677874486666664

> <ALOGPS_LOGS>
-1.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.251389406030864

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2267400183739792

> <JCHEM_PKA_STRONGEST_BASIC>
-1.34568639077838

> <JCHEM_POLAR_SURFACE_AREA>
174.64999999999998

> <JCHEM_REFRACTIVITY>
60.2481

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.52e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-Formyl-GAR

> <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      28.215 -15.989   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      29.755 -15.989   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      27.445 -17.323   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      30.525 -17.323   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      27.739 -14.525   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      26.406 -13.755   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      25.072 -14.525   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      23.532 -12.985   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      21.992 -14.525   0.000  0.00  0.00           O+0
HETATM   10  P   UNK     0      23.532 -14.525   0.000  0.00  0.00           P+0
HETATM   11  O   UNK     0      23.532 -16.065   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      28.985 -13.620   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      30.231 -14.525   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      31.565 -13.755   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0      32.899 -16.065   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      32.899 -14.525   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      34.232 -13.755   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      35.566 -14.525   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0      36.900 -13.755   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      38.233 -14.525   0.000  0.00  0.00           O+0
CONECT    1    5    2    3                                                  
CONECT    2    1   13    4                                                  
CONECT    3    1                                                            
CONECT    4    2                                                            
CONECT    5   12    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6   10                                                       
CONECT    8   10                                                            
CONECT    9   10                                                            
CONECT   10    7    8    9   11                                             
CONECT   11   10                                                            
CONECT   12    5   13                                                       
CONECT   13   12    2   14                                                  
CONECT   14   13   16                                                       
CONECT   15   16                                                            
CONECT   16   14   15   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

Synonyms

Value	Source
5'-Phosphoribosyl-N-formylglycinamide	ChEBI
N-Formyl-gar	ChEBI
N-Formylglycinamide ribonucleotide	ChEBI
N2-Formyl-N1-(5-phospho-D-ribosyl)glycinamide	ChEBI

Molecular Formula

C₈H₁₅N₂O₉P

Average Mass

314.1865

Monoisotopic Mass

314.0515166

IUPAC Name

{[(2R,3S,4R)-3,4-dihydroxy-5-(2-formamidoacetamido)oxolan-2-yl]methoxy}phosphonic acid

Traditional Name

N-Formyl-GAR

CAS Registry Number

349-34-8

SMILES

O[C@H]1[C@@H](O)C(NC(=O)CNC=O)O[C@@H]1COP(O)(O)=O

InChI Identifier

InChI=1S/C8H15N2O9P/c11-3-9-1-5(12)10-8-7(14)6(13)4(19-8)2-18-20(15,16)17/h3-4,6-8,13-14H,1-2H2,(H,9,11)(H,10,12)(H2,15,16,17)/t4-,6-,7-,8?/m1/s1

InChI Key

VDXLUNDMVKSKHO-ZRTZXPPTSA-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
N-formyl-alpha amino acid or derivatives
Alpha-amino acid amide
N-formyl-alpha-amino acid
N-substituted-alpha-amino acid
Alpha-amino acid or derivatives
Monosaccharide phosphate
Pentose monosaccharide
Monoalkyl phosphate
Organic phosphoric acid derivative
Alkyl phosphate
Monosaccharide
Phosphoric acid ester
Tetrahydrofuran
Secondary carboxylic acid amide
1,2-diol
Carboxamide group
Secondary alcohol
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Carbonyl group
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

glycinamide ribonucleotide (CHEBI:18272 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	6.52 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-3.9	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	174.65 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	60.25 m³·mol⁻¹	ChemAxon
Polarizability	25.66 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	splash10-0002-9330000000-47bd3a51454a22349c16	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-05n0-4391000000-a2e64d6206055bba1264	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0ads-9370000000-1d426c16f66d583bca44	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9400000000-e3430b27eecb4f2388bd	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-01tc-9623000000-d6c1bcb3aac926c857f6	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-59d3cfaf8e8cd6b90ec0	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a01410784072a771fa3f	2016-09-12	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

Not Available

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	1	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	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

Not Available

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

16048611

PDB ID

Not Available

ChEBI ID

18272

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Caperelli CA, Chettur G, Lin LY, Benkovic SJ: Purfication of glycineamide ribonucleotide transformylase. Biochem Biophys Res Commun. 1978 May 30;82(2):403-10. doi: 10.1016/0006-291x(78)90890-2. [PubMed:666851 ]
Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Bluthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novere N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasic I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttila M, Klipp E, Palsson BO, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB: A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492. [PubMed:18846089 ]
Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Sohngen C, Stelzer M, Thiele J, Schomburg D: BRENDA, the enzyme information system in 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D670-6. doi: 10.1093/nar/gkq1089. Epub 2010 Nov 9. [PubMed:21062828 ]

Showing metabocard for N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide (MMDBc0033116)

MOL for #<Metabolite:0x00007fecec016b30>

3D MOL for #<Metabolite:0x00007fecec016b30>

3D SDF for #<Metabolite:0x00007fecec016b30>

3D-SDF for #<Metabolite:0x00007fecec016b30>

PDB for #<Metabolite:0x00007fecec016b30>

3D PDB for #<Metabolite:0x00007fecec016b30>

SMILES for #<Metabolite:0x00007fecec016b30>

INCHI for #<Metabolite:0x00007fecec016b30>

Structure for #<Metabolite:0x00007fecec016b30>

3D Structure for #<Metabolite:0x00007fecec016b30>