NP-MRD: Showing NP-Card for 5'-Phosphoribosyl-N-formylglycinamide (NP0334683)

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Record Information

Version

2.0

Created at

2024-09-10 19:30:26 UTC

Updated at

2024-09-10 19:30:27 UTC

NP-MRD ID

NP0334683

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5'-Phosphoribosyl-N-formylglycinamide

Description

5'-Phosphoribosyl-N-formylglycinamide 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. 5'-Phosphoribosyl-N-formylglycinamide was first documented in 2014 (PMID: 24556226). Based on a literature review very few articles have been published on 5'-Phosphoribosyl-N-formylglycinamide (PMID: 38957115).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05252322022D          

 20 20  0  0  0  0            999 V2000
 9999.311810000.5633    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.597210000.1510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.882610000.5633    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.7787 9998.7115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.079110000.5633    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.5699 9998.7033    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.792510000.1510    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.507810000.5633    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10003.095510001.2766    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10004.221210000.1510    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.920210001.2766    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.692010000.6450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.024610000.1600    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.2795 9999.3754    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10001.1045 9999.3754    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10001.359410000.1600    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.5972 9999.3257    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.738710000.1510    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.453310000.5633    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.168110000.1510    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 12 13  1  0  0  0  0
 12 16  1  0  0  0  0
 13  1  1  6  0  0  0
 14  4  1  1  0  0  0
 16  5  1  6  0  0  0
 15  6  1  1  0  0  0
  2  3  1  0  0  0  0
 19 18  2  0  0  0  0
 20 19  1  0  0  0  0
  3 20  1  0  0  0  0
  2 17  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0334683

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1/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-/s2

> <INCHI_KEY>
VDXLUNDMVKSKHO-NHBCCFCANA-N

> <FORMULA>
C8H15N2O9P

> <MOLECULAR_WEIGHT>
314.187

> <EXACT_MASS>
314.051517069

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
25.691187600465334

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-3.867787448666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.251389402211153

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2263355568590275

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5302762200112932

> <JCHEM_POLAR_SURFACE_AREA>
174.64999999999998

> <JCHEM_REFRACTIVITY>
60.2481

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-formamidoacetamido)oxolan-2-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  N   UNK     0    8665.3828667.718   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0    8664.0488666.949   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8662.7148667.718   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8666.2548664.261   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8670.5488667.718   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    8669.5978664.246   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8671.8798666.949   0.000  0.00  0.00           O+0
HETATM    8  P   UNK     0    8673.2158667.718   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0    8672.4458669.050   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8674.5468666.949   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8673.9848669.050   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    8667.9588667.871   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0    8666.7138666.965   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8667.1888665.501   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8668.7288665.501   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8669.2048666.965   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0    8664.0488665.408   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0    8658.7128666.949   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0    8660.0468667.718   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0    8661.3808666.949   0.000  0.00  0.00           N+0
CONECT    1    2   13                                                       
CONECT    2    1    3   17                                                  
CONECT    3    2   20                                                       
CONECT    4   14                                                            
CONECT    5    7   16                                                       
CONECT    6   15                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
CONECT   12   13   16                                                       
CONECT   13   14   12    1                                                  
CONECT   14   13   15    4                                                  
CONECT   15   14   16    6                                                  
CONECT   16   15   12    5                                                  
CONECT   17    2                                                            
CONECT   18   19                                                            
CONECT   19   18   20                                                       
CONECT   20   19    3                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₈H₁₅N₂O₉P

Average Mass

314.1870 Da

Monoisotopic Mass

314.05152 Da

IUPAC Name

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

Traditional Name

[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-formamidoacetamido)oxolan-2-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1/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-/s2

InChI Key

VDXLUNDMVKSKHO-NHBCCFCANA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical 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
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

N-glycosyl compound (CHEBI:42411 )
ribose monophosphate (CHEBI:42411 )
amido monocarboxylic acid amide (CHEBI:42411 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-3.9	ChemAxon
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	-1.5	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	25.69 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00019642

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Poliakova Turan M, Riedo R, Medo M, Pozzato C, Friese-Hamim M, Koch JP, Coggins SA, Li Q, Kim B, Albers J, Aebersold DM, Zamboni N, Zimmer Y, Medova M: E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network. Cancer Res Commun. 2024 Jul 1;4(7):1863-1880. doi: 10.1158/2767-9764.CRC-23-0370. [PubMed:38957115 ]
Tan Y, Liu X, Lu C, He X, Li J, Xiao C, Jiang M, Yang J, Zhou K, Zhang Z, Zhang W, Lu A: Metabolic profiling reveals therapeutic biomarkers of processed Aconitum carmichaeli Debx in treating hydrocortisone induced kidney-yang deficiency syndrome rats. J Ethnopharmacol. 2014 Mar 28;152(3):585-93. doi: 10.1016/j.jep.2014.02.011. Epub 2014 Feb 17. [PubMed:24556226 ]

Showing NP-Card for 5'-Phosphoribosyl-N-formylglycinamide (NP0334683)

MOL for NP0334683 (5'-Phosphoribosyl-N-formylglycinamide)

3D MOL for NP0334683 (5'-Phosphoribosyl-N-formylglycinamide)

3D SDF for NP0334683 (5'-Phosphoribosyl-N-formylglycinamide)

3D-SDF for NP0334683 (5'-Phosphoribosyl-N-formylglycinamide)

PDB for NP0334683 (5'-Phosphoribosyl-N-formylglycinamide)

3D PDB for NP0334683 (5'-Phosphoribosyl-N-formylglycinamide)

SMILES for NP0334683 (5'-Phosphoribosyl-N-formylglycinamide)

INCHI for NP0334683 (5'-Phosphoribosyl-N-formylglycinamide)

Structure for NP0334683 (5'-Phosphoribosyl-N-formylglycinamide)

3D Structure for NP0334683 (5'-Phosphoribosyl-N-formylglycinamide)