NP-MRD: Showing NP-Card for 2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid (NP0330660)

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Record Information

Version

2.0

Created at

2022-09-12 16:13:29 UTC

Updated at

2022-09-12 16:13:29 UTC

NP-MRD ID

NP0330660

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid

Description

Glycinamide Ribonucleotide, also known as 5'-phosphoribosylglycinamide or GAR, 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. Glycinamide Ribonucleotide is a very strong basic compound (based on its pKa). Glycinamide Ribonucleotide exists in both E. 2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid is found in Apis cerana. Coli (prokaryote) and yeast (eukaryote).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 33  0  0  0  0  0  0  0  0999 V2000
   -5.3726    1.9031   -0.2412 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4966    1.1624    0.6380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2195    0.8475   -0.0462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0501    1.2294   -1.2259 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1854    0.1286    0.5919 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9713   -0.1570   -0.0940 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1476    0.3488    0.5102 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1283   -0.6024    0.5520 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5186   -0.0719    0.3325 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6831    0.5441   -0.8841 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3026    1.0790   -0.9607 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.2630    2.4725   -1.5627 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2352    0.0291   -1.8871 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9785    1.1046    0.5995 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7572   -1.6642   -0.4722 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3097   -2.8976   -0.1509 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7488   -1.6565   -0.2846 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0303   -2.3554    0.8748 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2026    2.9321   -0.2026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3088    1.5387   -1.2035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2583    1.8260    1.4942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0386    0.2628    0.9800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3253   -0.1902    1.5748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0038    0.2625   -1.1348 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0831   -1.1019    1.5401 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7339    0.6275    1.1664 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2181   -0.9343    0.4809 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5916    0.4442   -2.7070 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0063    2.0562    0.8877 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9716   -1.3508   -1.5020 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5782   -3.4101   -0.9741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2850   -2.0366   -1.1736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0096   -2.3703    1.0571 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 13  1  0
 11 14  1  0
 11 12  2  0
  8 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17  6  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  2 22  1  0
  5 23  1  0
  6 24  1  6
  8 25  1  1
  9 26  1  0
  9 27  1  0
 13 28  1  0
 14 29  1  0
 15 30  1  6
 16 31  1  0
 17 32  1  6
 18 33  1  0
M  END

ChEBI
  Mrv0541 02241222352D          

 18 18  0  0  1  0            999 V2000
    7.3235   -9.0935    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.9914   -8.6091    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5779   -9.8784    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.6585   -9.0947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4029   -9.8791    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.4433   -8.8404    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.8873  -10.5469    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0923  -10.5454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5392   -8.8380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5838   -7.7752    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.3683   -8.0308    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7994   -7.5196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8394   -6.9908    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3282   -8.5596    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6016   -8.0537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0595   -7.5666    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.4109   -7.9358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5131   -7.1737    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  6  0  0  0
  3  8  1  6  0  0  0
  1  9  1  1  0  0  0
 11 10  1  0  0  0  0
 12 10  2  0  0  0  0
 13 10  1  0  0  0  0
 14 10  1  0  0  0  0
  9 11  1  0  0  0  0
 15  6  1  0  0  0  0
 16 15  2  0  0  0  0
 17 15  1  0  0  0  0
 18 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0330660

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCC(=O)NC1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
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

> <INCHI_KEY>
OBQMLSFOUZUIOB-HJZCUYRDSA-N

> <FORMULA>
C7H15N2O8P

> <MOLECULAR_WEIGHT>
286.1764

> <EXACT_MASS>
286.056601978

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
23.69389940696378

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.40

> <JCHEM_LOGP>
-4.650616976017662

> <ALOGPS_LOGS>
-1.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.245768050847792

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2255744528280514

> <JCHEM_PKA_STRONGEST_BASIC>
8.141960108603826

> <JCHEM_POLAR_SURFACE_AREA>
171.57000000000002

> <JCHEM_REFRACTIVITY>
55.294799999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.46e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5'-phosphoribosylglycinamide

> <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      13.671 -16.975   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      14.917 -16.070   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      14.145 -18.440   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.163 -16.977   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      15.685 -18.441   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      17.627 -16.502   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      16.590 -19.688   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      13.239 -19.685   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      12.207 -16.498   0.000  0.00  0.00           C+0
HETATM   10  P   UNK     0      10.423 -14.514   0.000  0.00  0.00           P+0
HETATM   11  O   UNK     0      11.887 -14.991   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       8.959 -14.037   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      10.900 -13.049   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       9.946 -15.978   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      17.923 -15.034   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      16.911 -14.124   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      19.434 -14.813   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      19.624 -13.391   0.000  0.00  0.00           N+0
CONECT    1    2    3    9                                                  
CONECT    2    1    4                                                       
CONECT    3    1    5    8                                                  
CONECT    4    2    5    6                                                  
CONECT    5    3    4    7                                                  
CONECT    6    4   15                                                       
CONECT    7    5                                                            
CONECT    8    3                                                            
CONECT    9    1   11                                                       
CONECT   10   11   12   13   14                                             
CONECT   11   10    9                                                       
CONECT   12   10                                                            
CONECT   13   10                                                            
CONECT   14   10                                                            
CONECT   15    6   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Value	Source
5'-Phosphoribosylglycinamide	ChEBI
5'-Phosphoribosylglycineamide	ChEBI
GAR	ChEBI
Glycineamide ribonucleotide	ChEBI
Glycineamideribotide	ChEBI
N-Glycyl-5-O-phosphono-D-ribofuranosylamine	ChEBI
N1-(5-Phospho-D-ribosyl)glycinamide	ChEBI
Glycinamide ribonucleotide	ChEBI

Chemical Formula

C₇H₁₅N₂O₈P

Average Mass

286.1764 Da

Monoisotopic Mass

286.05660 Da

IUPAC Name

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

Traditional Name

5'-phosphoribosylglycinamide

CAS Registry Number

Not Available

SMILES

NCC(=O)NC1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

InChI Identifier

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

InChI Key

OBQMLSFOUZUIOB-HJZCUYRDSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Apis cerana	LOTUS Database	35616633

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
Alpha-amino acid amide
Alpha-amino acid or derivatives
Monosaccharide phosphate
Pentose monosaccharide
Monoalkyl phosphate
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Tetrahydrofuran
Secondary carboxylic acid amide
Secondary alcohol
Amino acid or derivatives
Carboxamide group
1,2-diol
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Organic nitrogen compound
Organic oxide
Primary aliphatic amine
Organopnictogen compound
Alcohol
Organonitrogen compound
Carbonyl group
Organooxygen compound
Amine
Organic oxygen compound
Hydrocarbon derivative
Primary amine
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

N-glycosyl compound (CHEBI:18349 )
ribose monophosphate (CHEBI:18349 )

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	-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	23.69 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

DB02236

Phenol Explorer Compound ID

Not Available

FoodDB 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

5459918

PDB ID

Not Available

ChEBI ID

18349

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid (NP0330660)

MOL for NP0330660 (2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid)

3D MOL for NP0330660 (2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid)

3D SDF for NP0330660 (2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid)

3D-SDF for NP0330660 (2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid)

PDB for NP0330660 (2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid)

3D PDB for NP0330660 (2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid)

SMILES for NP0330660 (2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid)

INCHI for NP0330660 (2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid)

Structure for NP0330660 (2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid)

3D Structure for NP0330660 (2-amino-n-[(3r,4s,5r)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid)