MiMeDB: Showing metabocard for N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide (MMDBc0056180)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:18:51 UTC

Update Date

2022-08-12 20:09:37 UTC

Metabolite ID

MMDBc0056180

Metabolite Identification

Common Name

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

Description

5'-P-ribosyl-N-formylglycineamide 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. Based on a literature review very few articles have been published on 5'-P-ribosyl-N-formylglycineamide.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222182D          

 24 24  0  0  1  0            999 V2000
   -1.6351   -1.4039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7911   -0.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1501   -0.7365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4555   -1.3177    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6116   -0.4778    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4857    0.0172    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2022    0.8421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6725   -0.1974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1626    1.3718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6329    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4175    0.5872    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.3643    1.4442    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1673    1.4888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6830    0.0460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5298   -0.8903    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  1  1  0  0  0
  5  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  1  1  0  0  0  0
  9  3  2  0  0  0  0
 10  5  2  0  0  0  0
  8 10  1  1  0  0  0
  3 11  1  4  0  0  0
  5 12  1  4  0  0  0
  6 13  1  6  0  0  0
  7 14  1  6  0  0  0
 18  2  1  0  0  0  0
 19  4  1  0  0  0  0
 19  8  1  0  0  0  0
 20 15  1  0  0  0  0
 20 16  1  0  0  0  0
 20 17  2  0  0  0  0
 20 18  1  0  0  0  0
  4 21  1  6  0  0  0
  6 22  1  1  0  0  0
  7 23  1  1  0  0  0
  8 24  1  6  0  0  0
M  CHG  2  11  -1  12  -1
M  END
> <DATABASE_ID>
MMDBc0056180

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP(O)(O)=O)O[C@@]([H])(N=C([O-])CN=C[O-])[C@]([H])(O)[C@]1([H])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)/p-2/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
VDXLUNDMVKSKHO-XVFCMESISA-L

> <FORMULA>
C8H13N2O9P

> <MOLECULAR_WEIGHT>
312.172

> <EXACT_MASS>
312.036964164

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
25.76803229837649

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-2-[(oxidomethylidene)amino]ethanecarboximidate

> <JCHEM_LOGP>
-3.4916885502316535

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.6061365268490273

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0740941991076514

> <JCHEM_PKA_STRONGEST_BASIC>
2.491042746546302

> <JCHEM_POLAR_SURFACE_AREA>
187.28999999999996

> <JCHEM_REFRACTIVITY>
82.3921

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
N-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-2-[(oxidomethylidene)amino]ethanecarboximidate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -3.052  -2.621   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.770   1.651   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.210  -1.053   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.147  -1.375   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -4.584  -2.460   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0      -0.615  -1.536   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0      -6.742  -0.892   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0      -2.773   0.032   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       7.844   1.572   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       6.855  -0.369   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       5.904   2.561   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       4.915   0.620   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM   20  P   UNK     0       6.379   1.096   0.000  0.00  0.00           P+0
HETATM   21  H   UNK     0       2.547   2.696   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0      -0.312   2.779   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0      -1.275   0.086   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.989  -1.662   0.000  0.00  0.00           H+0
CONECT    1    5    9                                                       
CONECT    2    4   18                                                       
CONECT    3    9   11                                                       
CONECT    4    2    6   19   21                                             
CONECT    5    1   10   12                                                  
CONECT    6    4    7   13   22                                             
CONECT    7    6    8   14   23                                             
CONECT    8    7   10   19   24                                             
CONECT    9    1    3                                                       
CONECT   10    5    8                                                       
CONECT   11    3                                                            
CONECT   12    5                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15   20                                                            
CONECT   16   20                                                            
CONECT   17   20                                                            
CONECT   18    2   20                                                       
CONECT   19    4    8                                                       
CONECT   20   15   16   17   18                                             
CONECT   21    4                                                            
CONECT   22    6                                                            
CONECT   23    7                                                            
CONECT   24    8                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END

Synonyms

Not Available

Molecular Formula

C₈H₁₃N₂O₉P

Average Mass

312.172

Monoisotopic Mass

312.036964164

IUPAC Name

N-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-2-[(oxidomethylidene)amino]ethanecarboximidate

Traditional Name

N-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-2-[(oxidomethylidene)amino]ethanecarboximidate

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP(O)(O)=O)O[C@@]([H])(N=C([O-])CN=C[O-])[C@]([H])(O)[C@]1([H])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)/p-2/t4-,6-,7-,8-/m1/s1

InChI Key

VDXLUNDMVKSKHO-XVFCMESISA-L

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-5-phosphate
Pentose phosphate
Alpha-amino acid amide
N-formyl-alpha-amino acid
N-formyl-alpha amino acid or derivatives
N-substituted-alpha-amino acid
Alpha-amino acid or derivatives
Monosaccharide phosphate
Monosaccharide
Alkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Oxolane
1,2-diol
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Hydrocarbon derivative
Alcohol
Carbonyl group
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Organic anion
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-3.5	ChemAxon
pKa (Strongest Acidic)	1.07	ChemAxon
pKa (Strongest Basic)	2.49	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	187.29 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	82.39 m³·mol⁻¹	ChemAxon
Polarizability	25.77 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	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
Bacteria	Firmicutes	83	Human feces; Human ; Human supragingival plaque; Catfish ; Cattle
Bacteria	Proteobacteria	251	Human ; Pig ; Human feces; River trout ; Turkey ; Chicken ; Cattle ; Rat ; Sheep
Bacteria	Actinobacteria	38	Human ; Human feces; Cattle
Eukaryota/Fungi	Ascomycota	2
Bacteria	Bacteroidetes	7	Human ; Human feces
Bacteria	Chlorobi	5
Archaea/Archaea	Euryarchaeota	30
Archaea/Archaea	Crenarchaeota	16
Bacteria	Spirochaetes	7	Human
Bacteria	Cyanobacteria	28
Archaea	Crenarchaeota	1
Bacteria	nah	1
Bacteria	Aquificae	1
Bacteria	Deinococcus-thermus	4
Archaea	Euryarchaeota	2
Bacteria	Thermotogae	3
Bacteria	Chloroflexi	2
Bacteria	Acidobacteria	1

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

90658924

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide (MMDBc0056180)

MOL for #<Metabolite:0x00005634c2a4bd28>

3D MOL for #<Metabolite:0x00005634c2a4bd28>

3D SDF for #<Metabolite:0x00005634c2a4bd28>

3D-SDF for #<Metabolite:0x00005634c2a4bd28>

PDB for #<Metabolite:0x00005634c2a4bd28>

3D PDB for #<Metabolite:0x00005634c2a4bd28>

SMILES for #<Metabolite:0x00005634c2a4bd28>

INCHI for #<Metabolite:0x00005634c2a4bd28>

Structure for #<Metabolite:0x00005634c2a4bd28>

3D Structure for #<Metabolite:0x00005634c2a4bd28>