NP-MRD: Showing NP-Card for 1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid (NP0278316)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-09 03:17:32 UTC

Updated at

2022-09-09 03:17:32 UTC

NP-MRD ID

NP0278316

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

SCHEMBL4943487 belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether). 1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid is found in Rothmannia longiflora. Based on a literature review very few articles have been published on SCHEMBL4943487.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 34  0  0  0  0  0  0  0  0999 V2000
    6.3496   -0.8026   -0.3248 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4072   -1.0608    0.0185 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3636   -0.4380   -0.3888 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4740    0.5934   -1.2966 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0286   -0.7922    0.0875 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9066   -0.1452   -0.3309 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6557   -0.4563    0.0975 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4432    0.2938   -0.4132 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9528    1.1876    0.5212 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1964    1.5821    0.1069 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2173    1.6478    1.2049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8694    2.5399    2.2120 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6929    0.5693   -0.9039 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6071    1.1158   -2.1643 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6672   -0.5502   -0.7097 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5250   -1.3016   -1.8638 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5302   -1.4455    0.9707 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6300   -2.1515    1.4430 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8962   -1.8218    0.9965 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8615   -2.4752    1.4403 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0357    1.5085   -1.1528 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0328    0.6735   -1.0564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1720    0.8049   -1.3598 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0901    2.5970   -0.3520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4404    0.6416    1.5619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1628    2.0350    0.7401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5536    2.4449    2.9212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7166    0.2118   -0.6787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5244    0.4156   -2.8678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9687   -1.1343    0.1619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4565   -1.6049   -2.1111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4233   -1.7405    1.3473 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5080   -2.9419    2.1434 H   0  0  0  0  0  0  0  0  0  0  0  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
  8 15  1  0
 15 16  1  0
 15 13  1  0
 13 14  1  0
  8  7  1  0
  7 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 19  5  1  0
  5  6  2  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
 13 10  1  0
  6  7  1  0
 12 27  1  0
 11 25  1  0
 11 26  1  0
 10 24  1  6
  8 23  1  6
 15 30  1  1
 16 31  1  0
 13 28  1  1
 14 29  1  0
 17 32  1  0
 18 33  1  0
  6 22  1  0
  4 21  1  0
  2  1  1  0
M  END


  Mrv1652309092205172D          

 19 20  0  0  1  0            999 V2000
    0.1067    5.5902    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1067    4.7652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8212    4.3527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    4.3527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    3.5277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    2.2902    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6548    1.8053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4248    0.3532    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3957    0.4394    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2197    0.3532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7743    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    3.5277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    4.3527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    4.7652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    5.5902    0.0000 O   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  2  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
  7 14  1  0  0  0  0
 14 15  1  1  0  0  0
  6 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
  4 18  1  0  0  0  0
 18 19  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0278316

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(=O)C(=C1)C(O)=N

> <INCHI_IDENTIFIER>
InChI=1S/C11H14N2O6/c12-10(18)5-3-13(2-1-6(5)15)11-9(17)8(16)7(4-14)19-11/h1-3,7-9,11,14,16-17H,4H2,(H2,12,18)/t7-,8-,9-,11-/m1/s1

> <INCHI_KEY>
MNWCUETVRXKWHC-TURQNECASA-N

> <FORMULA>
C11H14N2O6

> <MOLECULAR_WEIGHT>
270.241

> <EXACT_MASS>
270.085186179

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
25.024616753903633

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-4.171825431844806

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.593439031300477

> <JCHEM_PKA_STRONGEST_ACIDIC>
-1.4320024485039484

> <JCHEM_PKA_STRONGEST_BASIC>
11.46406441075312

> <JCHEM_POLAR_SURFACE_AREA>
134.31

> <JCHEM_REFRACTIVITY>
73.44379999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  N   UNK     0       0.199  10.435   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.199   8.895   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.533   8.125   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.134   8.125   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.134   6.585   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -2.468   5.815   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -2.468   4.275   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.222   3.370   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.698   1.905   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.793   0.659   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.739   0.820   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -3.238   1.905   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -4.143   0.659   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -3.714   3.370   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -5.179   3.846   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -3.802   6.585   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.802   8.125   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.468   8.895   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.468  10.435   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   18                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   16                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    7   15                                                  
CONECT   15   14                                                            
CONECT   16    6   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17    4   19                                                  
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₄N₂O₆

Average Mass

270.2410 Da

Monoisotopic Mass

270.08519 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(=O)C(=C1)C(O)=N

InChI Identifier

InChI=1S/C11H14N2O6/c12-10(18)5-3-13(2-1-6(5)15)11-9(17)8(16)7(4-14)19-11/h1-3,7-9,11,14,16-17H,4H2,(H2,12,18)/t7-,8-,9-,11-/m1/s1

InChI Key

MNWCUETVRXKWHC-TURQNECASA-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
Rothmannia longiflora	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glycosylamines

Alternative Parents

Substituents

N-glycosyl compound
Pentose monosaccharide
Nicotinamide
Pyridine carboxylic acid or derivatives
Dihydropyridine
Hydropyridine
Monosaccharide
Pyridine
Heteroaromatic compound
Oxolane
Vinylogous amide
Primary carboxylic acid amide
1,2-diol
Carboxamide group
Secondary alcohol
Cyclic ketone
Organoheterocyclic compound
Azacycle
Oxacycle
Carboxylic acid derivative
Primary alcohol
Alcohol
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organic nitrogen 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	-4.2	ChemAxon
pKa (Strongest Acidic)	-1.4	ChemAxon
pKa (Strongest Basic)	11.46	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	134.31 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	73.44 m³·mol⁻¹	ChemAxon
Polarizability	25.02 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

62924845

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14367030

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid (NP0278316)

MOL for NP0278316 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid)

3D MOL for NP0278316 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid)

3D SDF for NP0278316 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid)

3D-SDF for NP0278316 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid)

PDB for NP0278316 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid)

3D PDB for NP0278316 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid)

SMILES for NP0278316 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid)

INCHI for NP0278316 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid)

Structure for NP0278316 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid)

3D Structure for NP0278316 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxopyridine-3-carboximidic acid)