NP-MRD: Showing NP-Card for Crotonoside (NP0050701)

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Record Information

Version

2.0

Created at

2022-04-27 22:02:42 UTC

Updated at

2022-04-27 22:02:42 UTC

NP-MRD ID

NP0050701

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Crotonoside

Description

(2S,3S,4R,5S)-2-(6-amino-2-hydroxy-9H-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety. Crotonoside is found in Croton tiglium . Based on a literature review very few articles have been published on (2S,3S,4R,5S)-2-(6-amino-2-hydroxy-9H-purin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282200022D          

 20 22  0  0  1  0            999 V2000
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3687   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -1.2640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0992   -1.0091    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0992   -0.1841    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5683    0.3009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.4940    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -2.0486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9457   -2.2201    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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
  1  7  2  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  5 11  1  0  0  0  0
 12 11  1  1  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
 12 16  1  0  0  0  0
 16 17  1  6  0  0  0
 15 18  1  6  0  0  0
 14 19  1  1  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0050701

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC(=O)NC2=C1N=CN2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C10H13N5O5/c11-7-4-8(14-10(19)13-7)15(2-12-4)9-6(18)5(17)3(1-16)20-9/h2-3,5-6,9,16-18H,1H2,(H3,11,13,14,19)/t3-,5-,6-,9-/m0/s1

> <INCHI_KEY>
MIKUYHXYGGJMLM-GIMIYPNGSA-N

> <FORMULA>
C10H13N5O5

> <MOLECULAR_WEIGHT>
283.244

> <EXACT_MASS>
283.091668539

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
25.89848171128597

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-amino-9-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3,9-dihydro-2H-purin-2-one

> <ALOGPS_LOGP>
-1.85

> <JCHEM_LOGP>
-2.8386073953333333

> <ALOGPS_LOGS>
-1.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.465689532263529

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.857787908921358

> <JCHEM_PKA_STRONGEST_BASIC>
2.425640234456774

> <JCHEM_POLAR_SURFACE_AREA>
155.22

> <JCHEM_REFRACTIVITY>
64.1877

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.48e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-amino-9-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H-purin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  N   UNK     0       6.258   3.613   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       7.591   1.303   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       4.924   1.303   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       4.924   5.923   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.555  -1.114   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.650  -2.359   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.185  -1.884   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.185  -0.344   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -1.061   0.562   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -1.061  -2.789   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.126  -3.824   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       3.632  -4.144   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   11                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6    1    8                                                  
CONECT    8    7                                                            
CONECT    9    6   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    5   12                                                  
CONECT   12   11   13   16                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   19                                                  
CONECT   15   14   16   18                                                  
CONECT   16   15   12   17                                                  
CONECT   17   16                                                            
CONECT   18   15                                                            
CONECT   19   14   20                                                       
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₃N₅O₅

Average Mass

283.2440 Da

Monoisotopic Mass

283.09167 Da

IUPAC Name

6-amino-9-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3,9-dihydro-2H-purin-2-one

Traditional Name

6-amino-9-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H-purin-2-one

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)NC2=C1N=CN2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C10H13N5O5/c11-7-4-8(14-10(19)13-7)15(2-12-4)9-6(18)5(17)3(1-16)20-9/h2-3,5-6,9,16-18H,1H2,(H3,11,13,14,19)/t3-,5-,6-,9-/m0/s1

InChI Key

MIKUYHXYGGJMLM-GIMIYPNGSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Croton tiglium	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Not Available

Direct Parent

Purine nucleosides

Alternative Parents

Substituents

Purine nucleoside
N-glycosyl compound
Glycosyl compound
Pentose monosaccharide
6-aminopurine
Purinone
Imidazopyrimidine
Purine
Pyrimidone
Aminopyrimidine
Monosaccharide
Pyrimidine
N-substituted imidazole
Imidazole
Tetrahydrofuran
Heteroaromatic compound
Azole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Primary amine
Amine
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Primary alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	-1.8	ALOGPS
logP	-2.8	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	10.86	ChemAxon
pKa (Strongest Basic)	2.43	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	155.22 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	64.19 m³·mol⁻¹	ChemAxon
Polarizability	25.9 Å³	ChemAxon
Number of Rings	3	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

1266011

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

1549017

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Crotonoside (NP0050701)

MOL for NP0050701 (Crotonoside)

3D MOL for NP0050701 (Crotonoside)

3D SDF for NP0050701 (Crotonoside)

3D-SDF for NP0050701 (Crotonoside)

PDB for NP0050701 (Crotonoside)

3D PDB for NP0050701 (Crotonoside)

SMILES for NP0050701 (Crotonoside)

INCHI for NP0050701 (Crotonoside)

Structure for NP0050701 (Crotonoside)

3D Structure for NP0050701 (Crotonoside)