NP-MRD: Showing NP-Card for 5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid (NP0201905)

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Record Information

Version

2.0

Created at

2022-09-04 21:01:36 UTC

Updated at

2022-09-04 21:01:36 UTC

NP-MRD ID

NP0201905

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid

Description

ZINC11616872 belongs to the class of organic compounds known as 1-ribosyl-imidazolecarboxamides. These are organic compounds containing the imidazole ring linked to a ribose ring through a 1-2 bond. Based on a literature review very few articles have been published on ZINC11616872.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
    5.3138    0.3296   -1.6692 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3868   -0.4740   -1.0086 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3452   -0.9753   -0.4414 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4877   -2.0424    0.4292 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0445   -0.4123   -0.7259 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7613    0.6132   -1.5418 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4394    0.8433   -1.5453 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9010   -0.0613   -0.7131 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5123   -0.1864   -0.4070 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7050   -0.3967    0.9603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0008   -0.0393    1.2564 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9573   -1.1744    0.9639 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2425   -0.7910    1.2681 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3522    1.1502    0.3905 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2376    2.3007    1.1612 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2680    1.0993   -0.6593 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7837    1.1364   -1.9517 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8488   -0.8481   -0.1914 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7149   -1.9308    0.7317 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9148   -1.8802    1.3483 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9017    1.6186   -2.1158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9584   -1.0555   -0.9365 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1148    0.2383    2.3108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8507   -1.4445   -0.0958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6903   -2.0127    1.6564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8751   -0.8595    0.5063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3599    1.0479   -0.0623 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9670    2.3829    1.7928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6205    1.9659   -0.5311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9128    0.2340   -2.3346 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3120   -2.8506    0.4540 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0372   -1.7668    1.7008 H   0  0  0  0  0  0  0  0  0  0  0  0
 19 18  1  0
 18  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
  8 18  1  0
 16  9  1  0
 19 31  1  0
 19 32  1  0
  7 21  1  0
  9 22  1  6
 11 23  1  1
 12 24  1  0
 12 25  1  0
 13 26  1  0
 14 27  1  6
 15 28  1  0
 16 29  1  1
 17 30  1  0
  4 20  1  0
  2  1  1  0
M  END


  Mrv1652309042223012D          

 18 19  0  0  1  0            999 V2000
    1.9709    0.2323    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2564   -0.1802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5420    0.2323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2564   -1.0052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9239   -1.4901    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6689   -2.2748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8439   -2.2748    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3590   -2.9422    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6139   -3.7268    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0535   -4.2117    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0535   -5.0367    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6610   -5.4492    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7209   -3.7268    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5056   -3.9818    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4660   -2.9422    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9509   -2.2748    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5890   -1.4901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1956   -1.2352    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
  8 15  1  0  0  0  0
 15 16  1  6  0  0  0
  7 17  1  0  0  0  0
  4 17  2  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0201905

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=C(N=CN1[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O)C(O)=N

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N4O5/c10-7-4(8(11)17)12-2-13(7)9-6(16)5(15)3(1-14)18-9/h2-3,5-6,9,14-16H,1,10H2,(H2,11,17)/t3-,5-,6+,9+/m1/s1

> <INCHI_KEY>
RTRQQBHATOEIAF-ICKFSKTQSA-N

> <FORMULA>
C9H14N4O5

> <MOLECULAR_WEIGHT>
258.234

> <EXACT_MASS>
258.096419567

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
24.049167583570753

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-amino-1-[(2S,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-imidazole-4-carboximidic acid

> <JCHEM_LOGP>
-2.8772040849126306

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.454632651287135

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.624157925874234

> <JCHEM_PKA_STRONGEST_BASIC>
7.270919819532452

> <JCHEM_POLAR_SURFACE_AREA>
157.84

> <JCHEM_REFRACTIVITY>
69.2058

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
5-amino-1-[(2S,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  N   UNK     0       3.679   0.434   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       2.345  -0.336   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.012   0.434   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.345  -1.876   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       3.591  -2.782   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       3.115  -4.246   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       1.575  -4.246   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.670  -5.492   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.146  -6.957   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -0.100  -7.862   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.100  -9.402   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.234 -10.172   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.346  -6.957   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.810  -7.433   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -0.870  -5.492   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.775  -4.246   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.099  -2.782   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      -0.365  -2.306   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   17                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   17                                                  
CONECT    8    7    9   15                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    8   16                                                  
CONECT   16   15                                                            
CONECT   17    7    4   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₁₄N₄O₅

Average Mass

258.2340 Da

Monoisotopic Mass

258.09642 Da

IUPAC Name

5-amino-1-[(2S,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-imidazole-4-carboximidic acid

Traditional Name

5-amino-1-[(2S,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid

CAS Registry Number

Not Available

SMILES

NC1=C(N=CN1[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O)C(O)=N

InChI Identifier

InChI=1S/C9H14N4O5/c10-7-4(8(11)17)12-2-13(7)9-6(16)5(15)3(1-14)18-9/h2-3,5-6,9,14-16H,1,10H2,(H2,11,17)/t3-,5-,6+,9+/m1/s1

InChI Key

RTRQQBHATOEIAF-ICKFSKTQSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1-ribosyl-imidazolecarboxamides. These are organic compounds containing the imidazole ring linked to a ribose ring through a 1-2 bond.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Imidazole ribonucleosides and ribonucleotides

Sub Class

1-ribosyl-imidazolecarboxamides

Direct Parent

1-ribosyl-imidazolecarboxamides

Alternative Parents

Substituents

1-ribosyl-imidazolecarboxamide
N-glycosyl compound
Glycosyl compound
Pentose monosaccharide
2-heteroaryl carboxamide
Imidazole-4-carbonyl group
N-substituted imidazole
Monosaccharide
Aminoimidazole
Imidazole
Oxolane
Heteroaromatic compound
Azole
Vinylogous amide
Amino acid or derivatives
Carboxamide group
Primary carboxylic acid amide
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Carboxylic acid derivative
Amine
Alcohol
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	-2.9	ChemAxon
pKa (Strongest Acidic)	5.62	ChemAxon
pKa (Strongest Basic)	7.27	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	157.84 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	69.21 m³·mol⁻¹	ChemAxon
Polarizability	24.05 Å³	ChemAxon
Number of Rings	2	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

42066956

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid (NP0201905)

MOL for NP0201905 (5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid)

3D MOL for NP0201905 (5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid)

3D SDF for NP0201905 (5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid)

3D-SDF for NP0201905 (5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid)

PDB for NP0201905 (5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid)

3D PDB for NP0201905 (5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid)

SMILES for NP0201905 (5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid)

INCHI for NP0201905 (5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid)

Structure for NP0201905 (5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid)

3D Structure for NP0201905 (5-amino-1-[(2s,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]imidazole-4-carboximidic acid)