MiMeDB: Showing metabocard for 2-(Formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine (MMDBc0031141)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 00:36:54 UTC

Update Date

2022-08-31 17:58:46 UTC

Metabolite ID

MMDBc0031141

Metabolite Identification

Common Name

2-(Formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine

Description

2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine is an intermediate in purine metabolism. The enzyme phosphoribosylformylglycinamidine synthase [EC:6.3.5.3] catalyzes the production of this metabolite from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241222352D          

 20 20  0  0  0  0            999 V2000
    0.0625    2.0143    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3500    0.7448    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7625    0.0303    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4750    0.7448    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8875    0.0303    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6049    1.5293    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3194    1.9418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7299    1.5293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4444    1.9418    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1589    1.5293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8733    1.9418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5878    1.5293    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3023    1.9418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0168    1.5293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0339    1.5293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4628    1.5293    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7484    1.1168    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7484    1.9418    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7484    2.7668    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1589    0.7043    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  1  8  1  0  0  0  0
  6  2  1  0  0  0  0
  2  4  1  0  0  0  0
  4  8  1  0  0  0  0
  2  3  1  6  0  0  0
  4  5  1  6  0  0  0
  6  7  1  1  0  0  0
  7 15  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 20  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 15 18  1  0  0  0  0
 18 16  1  0  0  0  0
 18 17  1  0  0  0  0
 18 19  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031141

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H16N3O8P/c9-5(1-10-3-12)11-8-7(14)6(13)4(19-8)2-18-20(15,16)17/h3-4,6-8,13-14H,1-2H2,(H2,9,11)(H,10,12)(H2,15,16,17)/t4-,6-,7-,8?/m1/s1

> <INCHI_KEY>
PMCOGCVKOAOZQM-ZRTZXPPTSA-N

> <FORMULA>
C8H16N3O8P

> <MOLECULAR_WEIGHT>
313.2017

> <EXACT_MASS>
313.067501015

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
26.409320837922355

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.58

> <JCHEM_LOGP>
-4.139211972332413

> <ALOGPS_LOGS>
-1.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.2179514527651865

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.225940476160587

> <JCHEM_PKA_STRONGEST_BASIC>
7.381668547772353

> <JCHEM_POLAR_SURFACE_AREA>
181.42999999999998

> <JCHEM_REFRACTIVITY>
72.72009999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.65e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
FGAM

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       0.117   3.760   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.653   1.390   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.423   0.057   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.887   1.390   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.657   0.057   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.129   2.855   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.463   3.625   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.362   2.855   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.696   3.625   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       4.030   2.855   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.363   3.625   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       6.697   2.855   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       8.031   3.625   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       9.365   2.855   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -3.797   2.855   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -6.464   2.855   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -5.130   2.085   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0      -5.130   3.625   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0      -5.130   5.165   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0       4.030   1.315   0.000  0.00  0.00           N+0
CONECT    1    6    8                                                       
CONECT    2    6    4    3                                                  
CONECT    3    2                                                            
CONECT    4    2    8    5                                                  
CONECT    5    4                                                            
CONECT    6    1    2    7                                                  
CONECT    7    6   15                                                       
CONECT    8    1    4    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9   20   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15    7   18                                                       
CONECT   16   18                                                            
CONECT   17   18                                                            
CONECT   18   15   16   17   19                                             
CONECT   19   18                                                            
CONECT   20   10                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

Synonyms

Value	Source
1-(5'-Phosphoribosyl)-N-formylglycinamidine	ChEBI
2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine	ChEBI
2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine	ChEBI
5'-Phosphoribosyl-N-formylglycinamidine	ChEBI
5'-Phosphoribosylformylglycinamidine	ChEBI

Molecular Formula

C₈H₁₆N₃O₈P

Average Mass

313.2017

Monoisotopic Mass

313.067501015

IUPAC Name

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

Traditional Name

FGAM

CAS Registry Number

6157-85-3

SMILES

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

InChI Identifier

InChI=1S/C8H16N3O8P/c9-5(1-10-3-12)11-8-7(14)6(13)4(19-8)2-18-20(15,16)17/h3-4,6-8,13-14H,1-2H2,(H2,9,11)(H,10,12)(H2,15,16,17)/t4-,6-,7-,8?/m1/s1

InChI Key

PMCOGCVKOAOZQM-ZRTZXPPTSA-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
Monoalkyl phosphate
Organic phosphoric acid derivative
Alkyl phosphate
Phosphoric acid ester
Tetrahydrofuran
1,2-diol
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Amidine
Carboxylic acid amidine
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Carbonyl group
Organonitrogen compound
Alcohol
Organopnictogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

N-glycosyl compound (CHEBI:18413 )
ribose monophosphate (CHEBI:18413 )
carboxamidine (CHEBI:18413 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	8.65 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-4.1	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	7.38	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	181.43 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	72.72 m³·mol⁻¹	ChemAxon
Polarizability	26.41 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	Unknown
Eukaryota/Fungi	Ascomycota	1	Human feces	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

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

23657816

PDB ID

Not Available

ChEBI ID

18413

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 2-(Formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine (MMDBc0031141)

MOL for #<Metabolite:0x00007f12406263b8>

3D MOL for #<Metabolite:0x00007f12406263b8>

3D SDF for #<Metabolite:0x00007f12406263b8>

3D-SDF for #<Metabolite:0x00007f12406263b8>

PDB for #<Metabolite:0x00007f12406263b8>

3D PDB for #<Metabolite:0x00007f12406263b8>

SMILES for #<Metabolite:0x00007f12406263b8>

INCHI for #<Metabolite:0x00007f12406263b8>

Structure for #<Metabolite:0x00007f12406263b8>

3D Structure for #<Metabolite:0x00007f12406263b8>