Np mrd loader

Showing NP-Card for 6,8-Purinediol (NP0334047)

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Record Information
Version2.0
Created at2024-09-09 21:48:58 UTC
Updated at2024-09-09 21:48:59 UTC
NP-MRD IDNP0334047
Secondary Accession NumbersNone
Natural Product Identification
Common Name6,8-Purinediol
DescriptionComponent of hen egg yolk 6,8-Dihydroxypurine is an endogenous nucleoside found in human fluids. Purine bases are present in higher amounts in tumor-bearing patients compared to healthy controls. DNA hypermethylation is a common finding in malignant cells and has been explored as a therapeutic target for hypomethylating agents. When chemical bonds to DNA, the DNA becomes damaged and proper and complete replication cannot occur to make the normal intended cell. A DNA adduct is an abnormal piece of DNA covalently-bonded to a cancer-causing chemical. This has shown to be the start of a cancerous cell, or carcinogenesis. DNA adducts in scientific experiments are used as bio-markers and as such are themselves measured to reflect quantitatively, for comparison, the amount of cancer in the subject. (PMID: 3506820 , 17044778 , 17264127 , 16799933 ) [HMDB]
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0334047 (6,8-Purinediol)


  Mrv1652305221920442D          

 55 60  0  0  0  0            999 V2000
    1.4228    0.5625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0062   -0.2625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7083   -0.6750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2757    0.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7083    0.9750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4228   -0.2625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7908   -0.5174    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7908    0.8174    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7083   -1.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1007    0.1500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.3085    0.1500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2412    0.5625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8122   -0.2625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8122    0.5625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5267   -0.6750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5427    0.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5267    0.9750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.2412   -0.2625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.0276   -0.5174    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.0276    0.8174    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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    8.7177    0.1500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 54 48  1  0  0  0  0
 55 49  1  0  0  0  0
M  END
Download

3D MOL for NP0334047 (6,8-Purinediol)

Download
3D SDF for NP0334047 (6,8-Purinediol)

  Mrv1652305221920442D          

 55 60  0  0  0  0            999 V2000
    1.4228    0.5625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.1175   -1.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3085    0.1500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   12.2412   -0.2625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.0276   -0.5174    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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   11.5267   -1.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0334047

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=NC2=C(N1)N=CN=C2O.OC1=NC2=C(N1)N=CN=C2O.OC1=NC2=C(N1)N=CN=C2O.OC1=NC2=C(N1)N=CN=C2O.OC1=NC2=C(N1)N=CN=C2O

> <INCHI_IDENTIFIER>
InChI=1S/5C5H4N4O2/c5*10-4-2-3(6-1-7-4)9-5(11)8-2/h5*1H,(H3,6,7,8,9,10,11)

> <INCHI_KEY>
ZHWYDMYXJSUNAJ-UHFFFAOYSA-N

> <FORMULA>
C25H20N20O10

> <MOLECULAR_WEIGHT>
760.5543

> <EXACT_MASS>
760.16712696

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
13.019422193708234

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentakis(9H-purine-6,8-diol)

> <ALOGPS_LOGP>
-0.69

> <JCHEM_LOGP>
0.3750325856666668

> <ALOGPS_LOGS>
-1.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
10

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.850264272114362

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.378239595560755

> <JCHEM_PKA_STRONGEST_BASIC>
-0.6762347273969381

> <JCHEM_POLAR_SURFACE_AREA>
94.92

> <JCHEM_REFRACTIVITY>
35.333999999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.19e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pentakis(purine-6,8-dione)

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0334047 (6,8-Purinediol)
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PDB for NP0334047 (6,8-Purinediol)
HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0       2.656   1.050   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.012  -0.490   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.012   1.050   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.322  -1.260   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.381   0.280   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.322   1.820   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       2.656  -0.490   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      -1.476  -0.966   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0      -1.476   1.526   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       1.322  -2.800   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -3.921   0.280   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      12.753   1.050   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.086  -0.490   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.086   1.050   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.419  -1.260   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.716   0.280   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      11.419   1.820   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0      12.753  -0.490   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0       8.621  -0.966   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       8.621   1.526   0.000  0.00  0.00           N+0
HETATM   21  O   UNK     0      11.419  -2.800   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       6.176   0.280   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      22.850   1.050   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      20.183  -0.490   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      20.183   1.050   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      21.516  -1.260   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      17.813   0.280   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0      21.516   1.820   0.000  0.00  0.00           N+0
HETATM   29  N   UNK     0      22.850  -0.490   0.000  0.00  0.00           N+0
HETATM   30  N   UNK     0      18.718  -0.966   0.000  0.00  0.00           N+0
HETATM   31  N   UNK     0      18.718   1.526   0.000  0.00  0.00           N+0
HETATM   32  O   UNK     0      21.516  -2.800   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      16.273   0.280   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       2.656  -6.650   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -0.012  -8.190   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -0.012  -6.650   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       1.322  -8.960   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -2.381  -7.420   0.000  0.00  0.00           C+0
HETATM   39  N   UNK     0       1.322  -5.880   0.000  0.00  0.00           N+0
HETATM   40  N   UNK     0       2.656  -8.190   0.000  0.00  0.00           N+0
HETATM   41  N   UNK     0      -1.476  -8.666   0.000  0.00  0.00           N+0
HETATM   42  N   UNK     0      -1.476  -6.174   0.000  0.00  0.00           N+0
HETATM   43  O   UNK     0       1.322 -10.500   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      -3.921  -7.420   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      12.753  -6.650   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      10.086  -8.190   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      10.086  -6.650   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      11.419  -8.960   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       7.716  -7.420   0.000  0.00  0.00           C+0
HETATM   50  N   UNK     0      11.419  -5.880   0.000  0.00  0.00           N+0
HETATM   51  N   UNK     0      12.753  -8.190   0.000  0.00  0.00           N+0
HETATM   52  N   UNK     0       8.621  -8.666   0.000  0.00  0.00           N+0
HETATM   53  N   UNK     0       8.621  -6.174   0.000  0.00  0.00           N+0
HETATM   54  O   UNK     0      11.419 -10.500   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       6.176  -7.420   0.000  0.00  0.00           O+0
CONECT    1    6    7                                                       
CONECT    2    3    4    8                                                  
CONECT    3    2    6    9                                                  
CONECT    4    2    7   10                                                  
CONECT    5    8    9   11                                                  
CONECT    6    1    3                                                       
CONECT    7    1    4                                                       
CONECT    8    2    5                                                       
CONECT    9    3    5                                                       
CONECT   10    4                                                            
CONECT   11    5                                                            
CONECT   12   17   18                                                       
CONECT   13   14   15   19                                                  
CONECT   14   13   17   20                                                  
CONECT   15   13   18   21                                                  
CONECT   16   19   20   22                                                  
CONECT   17   12   14                                                       
CONECT   18   12   15                                                       
CONECT   19   13   16                                                       
CONECT   20   14   16                                                       
CONECT   21   15                                                            
CONECT   22   16                                                            
CONECT   23   28   29                                                       
CONECT   24   25   26   30                                                  
CONECT   25   24   28   31                                                  
CONECT   26   24   29   32                                                  
CONECT   27   30   31   33                                                  
CONECT   28   23   25                                                       
CONECT   29   23   26                                                       
CONECT   30   24   27                                                       
CONECT   31   25   27                                                       
CONECT   32   26                                                            
CONECT   33   27                                                            
CONECT   34   39   40                                                       
CONECT   35   36   37   41                                                  
CONECT   36   35   39   42                                                  
CONECT   37   35   40   43                                                  
CONECT   38   41   42   44                                                  
CONECT   39   34   36                                                       
CONECT   40   34   37                                                       
CONECT   41   35   38                                                       
CONECT   42   36   38                                                       
CONECT   43   37                                                            
CONECT   44   38                                                            
CONECT   45   50   51                                                       
CONECT   46   47   48   52                                                  
CONECT   47   46   50   53                                                  
CONECT   48   46   51   54                                                  
CONECT   49   52   53   55                                                  
CONECT   50   45   47                                                       
CONECT   51   45   48                                                       
CONECT   52   46   49                                                       
CONECT   53   47   49                                                       
CONECT   54   48                                                            
CONECT   55   49                                                            
MASTER        0    0    0    0    0    0    0    0   55    0  120    0
END

Download
3D PDB for NP0334047 (6,8-Purinediol)
Download
SMILES for NP0334047 (6,8-Purinediol)
OC1=NC2=C(N1)N=CN=C2O.OC1=NC2=C(N1)N=CN=C2O.OC1=NC2=C(N1)N=CN=C2O.OC1=NC2=C(N1)N=CN=C2O.OC1=NC2=C(N1)N=CN=C2O
Download
INCHI for NP0334047 (6,8-Purinediol)
InChI=1S/5C5H4N4O2/c5*10-4-2-3(6-1-7-4)9-5(11)8-2/h5*1H,(H3,6,7,8,9,10,11)
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View in JSmol
SynonymsNot Available
Chemical FormulaC25H20N20O10
Average Mass760.5543 Da
Monoisotopic Mass760.16713 Da
IUPAC Namepentakis(9H-purine-6,8-diol)
Traditional Namepentakis(purine-6,8-dione)
CAS Registry NumberNot Available
SMILES
OC1=NC2=C(N1)N=CN=C2O.OC1=NC2=C(N1)N=CN=C2O.OC1=NC2=C(N1)N=CN=C2O.OC1=NC2=C(N1)N=CN=C2O.OC1=NC2=C(N1)N=CN=C2O
InChI Identifier
InChI=1S/5C5H4N4O2/c5*10-4-2-3(6-1-7-4)9-5(11)8-2/h5*1H,(H3,6,7,8,9,10,11)
InChI KeyZHWYDMYXJSUNAJ-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hypoxanthines. Hypoxanthines are compounds containing the purine derivative 1H-purin-6(9H)-one. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassImidazopyrimidines  
Sub ClassPurines and purine derivatives  
Direct ParentHypoxanthines  
Alternative Parents
Substituents
  • 6-oxopurine
    • 

  • Hypoxanthine
    • 

  • Pyrimidone
    • 

  • Pyrimidine
    • 

  • Azole
    • 

  • Imidazole
    • 

  • Heteroaromatic compound
    • 

  • Vinylogous amide
    • 

  • Urea
    • 

  • Azacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkNot Available
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
logP-0.69ALOGPS
logP0.38ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)8.38ChemAxon
pKa (Strongest Basic)-0.68ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.92 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity35.33 m³·mol⁻¹ChemAxon
Polarizability13.02 ųChemAxon
Number of Rings10ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB019885  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References