NP-MRD: Showing NP-Card for (2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid (NP0175940)

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Record Information

Version

2.0

Created at

2022-09-03 13:31:10 UTC

Updated at

2022-09-03 13:31:10 UTC

NP-MRD ID

NP0175940

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid

Description

(2S,3R,5R,6R)-3,5-dihydroxy-6-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxane-2-carboxylic acid belongs to the class of organic compounds known as n-glucuronides. These are glucuronides in which the aglycone is linked to the carbohydrate unit through a N-glycosidic bond. (2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid is found in Streptomyces griseochromogenes. Based on a literature review very few articles have been published on (2S,3R,5R,6R)-3,5-dihydroxy-6-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxane-2-carboxylic acid.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309032215312D          

 19 20  0  0  1  0            999 V2000
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    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
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  8 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
  6 15  1  0  0  0  0
 15 16  1  1  0  0  0
  5 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
  2 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0175940

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1C[C@@H](O)[C@H](O[C@H]1N1C=CC(=N)N=C1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N3O6/c11-6-1-2-13(10(18)12-6)8-5(15)3-4(14)7(19-8)9(16)17/h1-2,4-5,7-8,14-15H,3H2,(H,16,17)(H2,11,12,18)/t4-,5-,7+,8-/m1/s1

> <INCHI_KEY>
PPFOLBMSDIVGQF-HXOWADHMSA-N

> <FORMULA>
C10H13N3O6

> <MOLECULAR_WEIGHT>
271.229

> <EXACT_MASS>
271.080435151

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
24.464527834132458

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,5R,6R)-3,5-dihydroxy-6-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxane-2-carboxylic acid

> <ALOGPS_LOGP>
-1.62

> <JCHEM_LOGP>
-1.6630409376880495

> <ALOGPS_LOGS>
-2.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
5.799040454079936

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4251278005717167

> <JCHEM_PKA_STRONGEST_BASIC>
2.293489090164053

> <JCHEM_POLAR_SURFACE_AREA>
146.67000000000002

> <JCHEM_REFRACTIVITY>
70.6901

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.87e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,5R,6R)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.334  -5.390   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.001 -11.550   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   19  N   UNK     0       0.000  -3.080   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   19                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   17                                                  
CONECT    6    5    7   15                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    8   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14    6   16                                                  
CONECT   16   15                                                            
CONECT   17    5   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17    2                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

View in JSmol

Synonyms

Value	Source
(2S,3R,5R,6R)-3,5-Dihydroxy-6-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxane-2-carboxylate	Generator

Chemical Formula

C₁₀H₁₃N₃O₆

Average Mass

271.2290 Da

Monoisotopic Mass

271.08044 Da

IUPAC Name

(2S,3R,5R,6R)-3,5-dihydroxy-6-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxane-2-carboxylic acid

Traditional Name

(2S,3R,5R,6R)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

O[C@@H]1C[C@@H](O)[C@H](O[C@H]1N1C=CC(=N)N=C1O)C(O)=O

InChI Identifier

InChI=1S/C10H13N3O6/c11-6-1-2-13(10(18)12-6)8-5(15)3-4(14)7(19-8)9(16)17/h1-2,4-5,7-8,14-15H,3H2,(H,16,17)(H2,11,12,18)/t4-,5-,7+,8-/m1/s1

InChI Key

PPFOLBMSDIVGQF-HXOWADHMSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces griseochromogenes	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-glucuronides. These are glucuronides in which the aglycone is linked to the carbohydrate unit through a N-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

N-glucuronides

Alternative Parents

Substituents

N-glucuronide
Glycosyl compound
N-glycosyl compound
Aminopyrimidine
Beta-hydroxy acid
Pyrimidone
Hydropyrimidine
Imidolactam
Pyrimidine
Pyran
Hydroxy acid
Oxane
Heteroaromatic compound
Amino acid or derivatives
Amino acid
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Amine
Alcohol
Carbonyl group
Organic nitrogen compound
Organic oxide
Primary amine
Hydrocarbon derivative
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	-1.6	ALOGPS
logP	-1.7	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	3.43	ChemAxon
pKa (Strongest Basic)	2.29	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	146.67 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	70.69 m³·mol⁻¹	ChemAxon
Polarizability	24.46 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

8882566

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10707225

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid (NP0175940)

MOL for NP0175940 ((2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid)

3D MOL for NP0175940 ((2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid)

3D SDF for NP0175940 ((2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid)

3D-SDF for NP0175940 ((2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid)

PDB for NP0175940 ((2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid)

3D PDB for NP0175940 ((2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid)

SMILES for NP0175940 ((2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid)

INCHI for NP0175940 ((2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid)

Structure for NP0175940 ((2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid)

3D Structure for NP0175940 ((2s,3r,5r,6r)-3,5-dihydroxy-6-(2-hydroxy-4-iminopyrimidin-1-yl)oxane-2-carboxylic acid)