NP-MRD: Showing NP-Card for 5'-Phosphoribosyl-alpha-N-formylglycineamidine (NP0334709)

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Record Information

Version

2.0

Created at

2024-09-10 19:37:35 UTC

Updated at

2024-09-10 19:37:35 UTC

NP-MRD ID

NP0334709

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5'-Phosphoribosyl-alpha-N-formylglycineamidine

Description

5'-Phosphoribosyl-alpha-N-formylglycineamidine 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. Based on a literature review very few articles have been published on 5'-Phosphoribosyl-alpha-N-formylglycineamidine.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05252322092D          

 20 20  0  0  0  0            999 V2000
    0.5678    1.1143    0.0000 C   0  0  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
    1.2352    0.6294    0.0000 C   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
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2857   -0.7365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6212    0.0172    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7706   -1.4039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5911   -1.3177    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0760   -1.9851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405    1.9462    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6251    2.2012    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0954    1.1616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5855    2.7308    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8965   -1.8989    0.0000 O   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
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  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
 10 11  2  0  0  0  0
  5 12  1  0  0  0  0
 12 13  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
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 16 19  2  0  0  0  0
 13  1  1  0  0  0  0
 11 20  1  4  0  0  0
M  END
> <DATABASE_ID>
NP0334709

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC=NCC(=N)NC1OC(COP(O)(O)=O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1/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)

> <INCHI_KEY>
PMCOGCVKOAOZQM-UHFFFAOYNA-N

> <FORMULA>
C8H16N3O8P

> <MOLECULAR_WEIGHT>
313.203

> <EXACT_MASS>
313.067501485

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
26.85797995839433

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(N-{3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl}carbamimidoyl)methyl]carboximidic acid

> <JCHEM_LOGP>
-3.811329961264807

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.4014315821599093

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0707203020350675

> <JCHEM_PKA_STRONGEST_BASIC>
6.917527624102583

> <JCHEM_POLAR_SURFACE_AREA>
184.92

> <JCHEM_REFRACTIVITY>
73.2418

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
N-[(N-{3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl}carbamimidoyl)methyl]carboximidic 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  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       2.735  -1.536   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       4.267  -1.375   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       4.893   0.032   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       5.172  -2.621   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       6.703  -2.460   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       7.609  -3.706   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.290  -0.290   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.971   3.157   0.000  0.00  0.00           O+0
HETATM   16  P   UNK     0      -3.436   3.633   0.000  0.00  0.00           P+0
HETATM   17  O   UNK     0      -4.900   4.109   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -3.911   2.168   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -2.960   5.098   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.140  -3.545   0.000  0.00  0.00           O+0
CONECT    1    2    3   13                                                  
CONECT    2    1                                                            
CONECT    3    1    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   12                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   20                                                       
CONECT   12    5   13                                                       
CONECT   13   12   14    1                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16                                                            
CONECT   20   11                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol

Synonyms

Value	Source
5'-Phosphoribosyl-a-N-formylglycineamidine	Generator
5'-Phosphoribosyl-α-N-formylglycineamidine	Generator

Chemical Formula

C₈H₁₆N₃O₈P

Average Mass

313.2030 Da

Monoisotopic Mass

313.06750 Da

IUPAC Name

N-[(N-{3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl}carbamimidoyl)methyl]carboximidic acid

Traditional Name

N-[(N-{3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl}carbamimidoyl)methyl]carboximidic acid

CAS Registry Number

Not Available

SMILES

OC=NCC(=N)NC1OC(COP(O)(O)=O)C(O)C1O

InChI Identifier

InChI=1/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)

InChI Key

PMCOGCVKOAOZQM-UHFFFAOYNA-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 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

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	-3.8	ChemAxon
pKa (Strongest Acidic)	1.07	ChemAxon
pKa (Strongest Basic)	6.92	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	184.92 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	73.24 m³·mol⁻¹	ChemAxon
Polarizability	26.86 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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 5'-Phosphoribosyl-alpha-N-formylglycineamidine (NP0334709)

MOL for NP0334709 (5'-Phosphoribosyl-alpha-N-formylglycineamidine)

3D MOL for NP0334709 (5'-Phosphoribosyl-alpha-N-formylglycineamidine)

3D SDF for NP0334709 (5'-Phosphoribosyl-alpha-N-formylglycineamidine)

3D-SDF for NP0334709 (5'-Phosphoribosyl-alpha-N-formylglycineamidine)

PDB for NP0334709 (5'-Phosphoribosyl-alpha-N-formylglycineamidine)

3D PDB for NP0334709 (5'-Phosphoribosyl-alpha-N-formylglycineamidine)

SMILES for NP0334709 (5'-Phosphoribosyl-alpha-N-formylglycineamidine)

INCHI for NP0334709 (5'-Phosphoribosyl-alpha-N-formylglycineamidine)

Structure for NP0334709 (5'-Phosphoribosyl-alpha-N-formylglycineamidine)

3D Structure for NP0334709 (5'-Phosphoribosyl-alpha-N-formylglycineamidine)