NP-MRD: Showing NP-Card for (s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid (NP0222598)

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Record Information

Version

1.0

Created at

2022-09-06 00:28:25 UTC

Updated at

2022-09-06 00:28:25 UTC

NP-MRD ID

NP0222598

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid

Description

Polyoxin c belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives. (s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid is found in Streptomyces cacaoi. Based on a literature review very few articles have been published on Polyoxin c.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309062202282D          

 22 23  0  0  1  0            999 V2000
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4324   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9173   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7378   -3.6695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0733   -2.9158    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5817   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667   -5.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7613   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4559   -4.0144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  6  2  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
  9 17  1  0  0  0  0
 17 18  2  0  0  0  0
  8 19  1  0  0  0  0
 19 20  1  6  0  0  0
 19 21  1  0  0  0  0
  6 21  1  0  0  0  0
 21 22  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0222598

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H]([C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(CO)C(O)=NC1=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H15N3O8/c12-4(10(19)20)7-5(16)6(17)9(22-7)14-1-3(2-15)8(18)13-11(14)21/h1,4-7,9,15-17H,2,12H2,(H,19,20)(H,13,18,21)/t4-,5-,6+,7+,9+/m0/s1

> <INCHI_KEY>
TZQKKPBFBDTCRN-AJDRIWCOSA-N

> <FORMULA>
C11H15N3O8

> <MOLECULAR_WEIGHT>
317.254

> <EXACT_MASS>
317.085914455

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
27.826803379638747

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-2-[(2R,3S,4R,5R)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxo-1,2-dihydropyrimidin-1-yl]oxolan-2-yl]acetic acid

> <JCHEM_LOGP>
-5.612629800723125

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.035310234080485

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.477341305945938

> <JCHEM_PKA_STRONGEST_BASIC>
8.231293873013689

> <JCHEM_POLAR_SURFACE_AREA>
186.14

> <JCHEM_REFRACTIVITY>
66.50649999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  N   UNK     0       2.667  -0.000   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.580  -3.215   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       3.009  -5.926   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       4.540  -5.765   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.446  -7.011   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.977  -6.850   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       7.604  -5.443   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.819  -8.417   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       5.724  -9.663   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0       3.288  -8.578   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       2.382  -7.333   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.851  -7.494   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.342  -5.926   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -1.377  -2.739   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    2    7   21                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   19                                                  
CONECT    9    8   10   17                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16    9   18                                                  
CONECT   18   17                                                            
CONECT   19    8   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19    6   22                                                  
CONECT   22   21                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₅N₃O₈

Average Mass

317.2540 Da

Monoisotopic Mass

317.08591 Da

IUPAC Name

(2S)-2-amino-2-[(2R,3S,4R,5R)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxo-1,2-dihydropyrimidin-1-yl]oxolan-2-yl]acetic acid

Traditional Name

(S)-amino[(2R,3S,4R,5R)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid

CAS Registry Number

Not Available

SMILES

N[C@@H]([C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=C(CO)C(O)=NC1=O)C(O)=O

InChI Identifier

InChI=1S/C11H15N3O8/c12-4(10(19)20)7-5(16)6(17)9(22-7)14-1-3(2-15)8(18)13-11(14)21/h1,4-7,9,15-17H,2,12H2,(H,19,20)(H,13,18,21)/t4-,5-,6+,7+,9+/m0/s1

InChI Key

TZQKKPBFBDTCRN-AJDRIWCOSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces cacaoi	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

5'-deoxyribonucleosides

Sub Class

Not Available

Direct Parent

5'-deoxyribonucleosides

Alternative Parents

Substituents

5'-deoxyribonucleoside
Glycosyl compound
N-glycosyl compound
Alpha-amino acid
Alpha-amino acid or derivatives
L-alpha-amino acid
Pyrimidone
Hydropyrimidine
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Amino acid or derivatives
Lactam
Amino acid
Urea
Secondary alcohol
Oxacycle
Azacycle
Carboxylic acid derivative
Carboxylic acid
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Primary aliphatic amine
Hydrocarbon derivative
Alcohol
Organic oxide
Organopnictogen compound
Amine
Organic oxygen compound
Carbonyl group
Organonitrogen compound
Organooxygen compound
Primary alcohol
Primary amine
Organic nitrogen compound
Aromatic alcohol
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	-5.6	ChemAxon
pKa (Strongest Acidic)	1.48	ChemAxon
pKa (Strongest Basic)	8.23	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	186.14 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	66.51 m³·mol⁻¹	ChemAxon
Polarizability	27.83 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

146921

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

167956

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid (NP0222598)

MOL for NP0222598 ((s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid)

3D MOL for NP0222598 ((s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid)

3D SDF for NP0222598 ((s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid)

3D-SDF for NP0222598 ((s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid)

PDB for NP0222598 ((s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid)

3D PDB for NP0222598 ((s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid)

SMILES for NP0222598 ((s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid)

INCHI for NP0222598 ((s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid)

Structure for NP0222598 ((s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid)

3D Structure for NP0222598 ((s)-amino[(2r,3s,4r,5r)-3,4-dihydroxy-5-[4-hydroxy-5-(hydroxymethyl)-2-oxopyrimidin-1-yl]oxolan-2-yl]acetic acid)