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Showing NP-Card for Zapotidine (NP0067737)

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Record Information
Version2.0
Created at2022-04-28 12:35:22 UTC
Updated at2022-04-28 12:35:22 UTC
NP-MRD IDNP0067737
Secondary Accession NumbersNone
Natural Product Identification
Common NameZapotidine
DescriptionZapotidine belongs to the class of organic compounds known as pyrimidinethiones. Pyrimidinethiones are compounds containing a pyrimidine ring that bears a thioketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Zapotidine is a moderately basic compound (based on its pKa). Outside of the human body, Zapotidine has been detected, but not quantified in, pomes. Zapotidine is found in Casimiroa edulis and Casimiroa edulis Llave et Lex . This could make zapotidine a potential biomarker for the consumption of these foods.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0067737 (Zapotidine)


  Mrv0541 05061305122D          

 11 12  0  0  0  0            999 V2000
    2.7845    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    3.1729    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  6  2  1  0  0  0  0
  6  4  2  0  0  0  0
  8  4  1  0  0  0  0
  8  5  2  0  0  0  0
  9  1  1  0  0  0  0
  9  3  1  0  0  0  0
  9  7  1  0  0  0  0
 10  5  1  0  0  0  0
 10  6  1  0  0  0  0
 10  7  1  0  0  0  0
 11  7  2  0  0  0  0
M  END
Download

3D MOL for NP0067737 (Zapotidine)

     RDKit          3D

 20 21  0  0  0  0  0  0  0  0999 V2000
   -2.6018    0.8245   -0.2302 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3291    0.2495    0.0874 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9881   -1.0750   -0.3648 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3406   -1.0653   -1.0629 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3683   -0.4413   -0.2178 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7573   -0.6567   -0.1823 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2305    0.1977    0.7369 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2011    0.8949    1.2369 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0446    0.5098    0.6569 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297    0.9075    0.8525 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6896    2.0717    1.8940 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3826    0.0649   -0.3984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5403    1.5538   -1.0784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9261    1.4055    0.6830 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8433   -1.7249    0.5492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7936   -1.5044   -1.0073 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2326   -0.3907   -1.9567 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6345   -2.0900   -1.3981 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3023   -1.3819   -0.7946 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3124    1.6503    1.9948 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10  2  1  0
  9  5  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  6 19  1  0
  8 20  1  0
M  END
Download

3D SDF for NP0067737 (Zapotidine)


  Mrv0541 05061305122D          

 11 12  0  0  0  0            999 V2000
    2.7845    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    3.1729    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  6  2  1  0  0  0  0
  6  4  2  0  0  0  0
  8  4  1  0  0  0  0
  8  5  2  0  0  0  0
  9  1  1  0  0  0  0
  9  3  1  0  0  0  0
  9  7  1  0  0  0  0
 10  5  1  0  0  0  0
 10  6  1  0  0  0  0
 10  7  1  0  0  0  0
 11  7  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0067737

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1CCC2=CN=CN2C1=S

> <INCHI_IDENTIFIER>
InChI=1S/C7H9N3S/c1-9-3-2-6-4-8-5-10(6)7(9)11/h4-5H,2-3H2,1H3

> <INCHI_KEY>
OXVNSOXLMCVHBU-UHFFFAOYSA-N

> <FORMULA>
C7H9N3S

> <MOLECULAR_WEIGHT>
167.231

> <EXACT_MASS>
167.051717993

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
17.251312247345545

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-methyl-5H,6H,7H,8H-imidazo[1,5-c]pyrimidine-5-thione

> <ALOGPS_LOGP>
0.63

> <JCHEM_LOGP>
-0.09055075166666637

> <ALOGPS_LOGS>
-2.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
2.746152280742804

> <JCHEM_POLAR_SURFACE_AREA>
21.060000000000002

> <JCHEM_REFRACTIVITY>
48.041599999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.04e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-methyl-7H,8H-imidazo[1,5-c]pyrimidine-5-thione

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for NP0067737 (Zapotidine)

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PDB for NP0067737 (Zapotidine)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       5.198   4.383   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.530   1.303   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.864   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.268   1.597   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.268   4.089   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.197   2.073   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.530   4.383   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -1.173   2.843   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       3.864   3.613   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       1.197   3.613   0.000  0.00  0.00           N+0
HETATM   11  S   UNK     0       2.530   5.923   0.000  0.00  0.00           S+0
CONECT    1    9                                                            
CONECT    2    3    6                                                       
CONECT    3    2    9                                                       
CONECT    4    6    8                                                       
CONECT    5    8   10                                                       
CONECT    6    2    4   10                                                  
CONECT    7    9   10   11                                                  
CONECT    8    4    5                                                       
CONECT    9    1    3    7                                                  
CONECT   10    5    6    7                                                  
CONECT   11    7                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END

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3D PDB for NP0067737 (Zapotidine)
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SMILES for NP0067737 (Zapotidine)
CN1CCC2=CN=CN2C1=S
Download
INCHI for NP0067737 (Zapotidine)
InChI=1S/C7H9N3S/c1-9-3-2-6-4-8-5-10(6)7(9)11/h4-5H,2-3H2,1H3
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View in JSmol
Synonyms
ValueSource
6-Methylimidazo[1,5-c]tetrahydropyrimidine-5-thioneHMDB
Chemical FormulaC7H9N3S
Average Mass167.2310 Da
Monoisotopic Mass167.05172 Da
IUPAC Name6-methyl-5H,6H,7H,8H-imidazo[1,5-c]pyrimidine-5-thione
Traditional Name6-methyl-7H,8H-imidazo[1,5-c]pyrimidine-5-thione
CAS Registry NumberNot Available
SMILES
CN1CCC2=CN=CN2C1=S
InChI Identifier
InChI=1S/C7H9N3S/c1-9-3-2-6-4-8-5-10(6)7(9)11/h4-5H,2-3H2,1H3
InChI KeyOXVNSOXLMCVHBU-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Casimiroa edulisLOTUS Database
Casimiroa edulis Llave et LexPlant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidinethiones. Pyrimidinethiones are compounds containing a pyrimidine ring that bears a thioketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassDiazines  
Sub ClassPyrimidines and pyrimidine derivatives  
Direct ParentPyrimidinethiones  
Alternative Parents
Substituents
  • Pyrimidinethione
    • 

  • N-substituted imidazole
    • 

  • Heteroaromatic compound
    • 

  • Imidazole
    • 

  • Azole
    • 

  • Thiourea
    • 

  • Azacycle
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organosulfur compound
    • 

  • Organonitrogen compound
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.63ALOGPS
logP-0.091ChemAxon
logS-2.3ALOGPS
pKa (Strongest Basic)2.75ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area21.06 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity48.04 m³·mol⁻¹ChemAxon
Polarizability17.25 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0030383  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB002234  
KNApSAcK IDC00025547  
Chemspider ID30776830  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12445018  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available