NP-MRD: Showing NP-Card for 5-Phosphoribosylglycineamide (NP0054946)

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Record Information

Version

2.0

Created at

2022-04-28 01:08:33 UTC

Updated at

2022-04-28 01:08:33 UTC

NP-MRD ID

NP0054946

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-Phosphoribosylglycineamide

Description

2-Amino-N-[(2S,3R,4R,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid 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. 5-Phosphoribosylglycineamide is found in Arabidopsis thaliana and Escherichia coli. Based on a literature review very few articles have been published on 2-amino-N-[(2S,3R,4R,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 33  0  0  0  0  0  0  0  0999 V2000
    5.4200    1.4744    0.1688 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6062    0.4190   -0.3665 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2323    0.4863    0.1895 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9748    1.4039    1.0081 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2227   -0.4611   -0.1886 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9164   -0.3575    0.3713 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0796   -0.1502   -0.5613 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1541   -0.9397   -0.2668 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4832   -0.3022   -0.5128 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6944    0.8432    0.2160 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1914    1.5297   -0.0843 P   0  0  2  0  0  5  0  0  0  0  0  0
   -4.9006    1.7646    1.2278 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1286    0.4911   -1.0691 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0760    3.0128   -0.8825 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9805   -1.4367    1.1522 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3534   -0.4576    2.0960 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5294   -1.5641    1.2011 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8831   -2.7549    0.5495 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8757    1.1580    1.0767 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9011    2.3518    0.3583 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0510   -0.5756   -0.0847 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5473    0.4430   -1.4774 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4354   -1.2207   -0.8659 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8620    0.5180    1.0816 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0723   -1.8592   -0.9137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5504   -0.0498   -1.5899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2929   -1.0148   -0.3043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2273   -0.3491   -0.5418 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6382    3.7032   -0.4467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4926   -2.3882    1.3323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0388    0.4357    1.8105 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9309   -1.5219    2.2264 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9658   -2.6318   -0.4209 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
 11 10  1  1
 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  1
  8 25  1  6
  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  1
 18 33  1  0
M  END


  Mrv1652304282203082D          

 18 18  0  0  1  0            999 V2000
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    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
   -0.0997    0.6294    0.0000 O   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
    0.0059   -1.5764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8264   -1.6626    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4790   -2.2438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -2.9975    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    3.1768    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    4.0018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1072    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4572    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  4  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 11  1  1  0  0  0
  2 12  1  6  0  0  0
  1 13  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0054946

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCC(=O)N[C@H]1O[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-CEGFXJEYSA-N

> <FORMULA>
C7H15N2O8P

> <MOLECULAR_WEIGHT>
286.177

> <EXACT_MASS>
286.056602449

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
24.046942293478555

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.40

> <JCHEM_LOGP>
-4.650616976017661

> <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>
171.57

> <JCHEM_REFRACTIVITY>
55.294799999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.46e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3R,4R,5S)-5-(2-aminoacetamido)-3,4-dihydroxyoxolan-2-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.186   1.175   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      -0.615  -1.536   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.011  -2.943   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.543  -3.104   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.894  -4.188   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -0.268  -5.595   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       2.735  -1.536   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.393   4.390   0.000  0.00  0.00           O+0
HETATM   15  P   UNK     0       2.393   5.930   0.000  0.00  0.00           P+0
HETATM   16  O   UNK     0       2.393   7.470   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.933   5.930   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.853   5.930   0.000  0.00  0.00           O+0
CONECT    1    2    5   13                                                  
CONECT    2    1    3   12                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4    1                                                       
CONECT    6    4    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9                                                            
CONECT   11    3                                                            
CONECT   12    2                                                            
CONECT   13    1   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   15                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Value	Source
2-Amino-N-[(2S,3R,4R,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]ethanimidate	Generator

Chemical Formula

C₇H₁₅N₂O₈P

Average Mass

286.1770 Da

Monoisotopic Mass

286.05660 Da

IUPAC Name

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

Traditional Name

[(2R,3R,4R,5S)-5-(2-aminoacetamido)-3,4-dihydroxyoxolan-2-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

NCC(=O)N[C@H]1O[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-CEGFXJEYSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Arabidopsis thaliana	Plant	KNApSAcK
Escherichia coli	Bacteria	KNApSAcK

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-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Tetrahydrofuran
Secondary alcohol
1,2-diol
Oxacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organonitrogen compound
Primary aliphatic amine
Amine
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

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	24.05 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

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

163021151

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for 5-Phosphoribosylglycineamide (NP0054946)

MOL for NP0054946 (5-Phosphoribosylglycineamide)

3D MOL for NP0054946 (5-Phosphoribosylglycineamide)

3D SDF for NP0054946 (5-Phosphoribosylglycineamide)

3D-SDF for NP0054946 (5-Phosphoribosylglycineamide)

PDB for NP0054946 (5-Phosphoribosylglycineamide)

3D PDB for NP0054946 (5-Phosphoribosylglycineamide)

SMILES for NP0054946 (5-Phosphoribosylglycineamide)

INCHI for NP0054946 (5-Phosphoribosylglycineamide)

Structure for NP0054946 (5-Phosphoribosylglycineamide)

3D Structure for NP0054946 (5-Phosphoribosylglycineamide)