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Showing NP-Card for xanthopterin-b2 (NP0225257)

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Record Information
Version2.0
Created at2022-09-06 03:55:54 UTC
Updated at2022-09-06 03:55:54 UTC
NP-MRD IDNP0225257
Secondary Accession NumbersNone
Natural Product Identification
Common Namexanthopterin-b2
DescriptionXanthopterin-B2 belongs to the class of organic compounds known as pteridines and derivatives. These are polycyclic aromatic compounds containing a pteridine moiety, which consists of a pyrimidine fused to a pyrazine ring to form pyrimido(4,5-b)pyrazine. xanthopterin-b2 is found in Bombyx mori. Xanthopterin-B2 is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0225257 (xanthopterin-b2)


  Mrv1533004161504502D          

 17 18  0  0  0  0            999 V2000
   -2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 O   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 O   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
    0.0000   -1.6500    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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -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  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 N   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 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
  8 16  1  0  0  0  0
 16 17  2  0  0  0  0
M  END
Download

3D MOL for NP0225257 (xanthopterin-b2)

     RDKit          3D

 27 28  0  0  0  0  0  0  0  0999 V2000
   -2.9531   -0.5651   -0.9834 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7373   -1.4531    0.2507 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9541   -1.8280    0.7804 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9715   -0.6025    1.2121 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4821   -0.3460    2.3059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6448   -0.0767    0.8812 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1133   -0.3566   -0.2848 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1562    0.0983   -0.7029 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8742    0.8880    0.1820 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0870    1.3357   -0.1898 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5713    1.0128   -1.3949 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7081    1.4312   -1.7460 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9152    0.2501   -2.2902 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7003   -0.2110   -1.9443 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0356   -0.9284   -2.7346 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3429    1.2233    1.4642 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0546    0.7506    1.8657 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0395    0.5036   -0.6862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0665   -0.6612   -1.6101 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9014   -0.8578   -1.4772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1756   -2.3640   -0.0012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9089   -2.7435    1.1212 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6643    1.9394    0.4558 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3121    0.0072   -3.2321 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8880    1.8077    2.1040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5573    1.6231    2.2260 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1955    0.1229    2.7937 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 16  1  0
 16 17  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  2  0
 17  6  1  0
 14  8  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  6
  3 22  1  0
 16 25  1  0
 17 26  1  0
 17 27  1  0
 10 23  1  0
 13 24  1  0
M  END
Download

3D SDF for NP0225257 (xanthopterin-b2)


  Mrv1533004161504502D          

 17 18  0  0  0  0            999 V2000
   -2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 O   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 O   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
    0.0000   -1.6500    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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -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  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 N   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 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
  8 16  1  0  0  0  0
 16 17  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0225257

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(O)C(=O)C1=NC2=C(NC1)NC(=O)NC2=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H10N4O4/c1-3(14)6(15)4-2-10-7-5(11-4)8(16)13-9(17)12-7/h3,14H,2H2,1H3,(H3,10,12,13,16,17)

> <INCHI_KEY>
PINNBMAOEJRIQL-UHFFFAOYSA-N

> <FORMULA>
C9H10N4O4

> <MOLECULAR_WEIGHT>
238.203

> <EXACT_MASS>
238.070204818

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
21.771719966115246

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-(2-hydroxypropanoyl)-1,2,3,4,7,8-hexahydropteridine-2,4-dione

> <ALOGPS_LOGP>
-0.93

> <JCHEM_LOGP>
-1.0977740696666665

> <ALOGPS_LOGS>
-2.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.290611172792556

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.267104089269479

> <JCHEM_PKA_STRONGEST_BASIC>
-1.6266420549563692

> <JCHEM_POLAR_SURFACE_AREA>
119.88999999999999

> <JCHEM_REFRACTIVITY>
65.51759999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.92e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
xanthopterin-B2

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0225257 (xanthopterin-b2)

Download
PDB for NP0225257 (xanthopterin-b2)
HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -2.667  -4.620   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  N   UNK     0       0.000  -3.080   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.000  -0.000   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       2.667  -0.000   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       4.001  -2.310   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   16                                                  
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10    6                                                       
CONECT   12    9   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15    8   17                                                  
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

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3D PDB for NP0225257 (xanthopterin-b2)
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SMILES for NP0225257 (xanthopterin-b2)
CC(O)C(=O)C1=NC2=C(NC1)NC(=O)NC2=O
Download
INCHI for NP0225257 (xanthopterin-b2)
InChI=1S/C9H10N4O4/c1-3(14)6(15)4-2-10-7-5(11-4)8(16)13-9(17)12-7/h3,14H,2H2,1H3,(H3,10,12,13,16,17)
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View in JSmol
Synonyms
ValueSource
1-(7,8-Dihydro-2,4-dihydroxypteridin-6-yl)-2-hydroxypropan-1-oneChEBI
Chemical FormulaC9H10N4O4
Average Mass238.2030 Da
Monoisotopic Mass238.07020 Da
IUPAC Name6-(2-hydroxypropanoyl)-1,2,3,4,7,8-hexahydropteridine-2,4-dione
Traditional Namexanthopterin-B2
CAS Registry NumberNot Available
SMILES
CC(O)C(=O)C1=NC2=C(NC1)NC(=O)NC2=O
InChI Identifier
InChI=1S/C9H10N4O4/c1-3(14)6(15)4-2-10-7-5(11-4)8(16)13-9(17)12-7/h3,14H,2H2,1H3,(H3,10,12,13,16,17)
InChI KeyPINNBMAOEJRIQL-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Bombyx moriLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pteridines and derivatives. These are polycyclic aromatic compounds containing a pteridine moiety, which consists of a pyrimidine fused to a pyrazine ring to form  pyrimido(4,5-b)pyrazine.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPteridines and derivatives  
Sub ClassNot Available
Direct ParentPteridines and derivatives  
Alternative Parents
Substituents
  • Pteridine
    • 

  • Pyrimidone
    • 

  • Secondary aliphatic/aromatic amine
    • 

  • Acyloin
    • 

  • Pyrimidine
    • 

  • Alpha-hydroxy ketone
    • 

  • Vinylogous amide
    • 

  • Heteroaromatic compound
    • 

  • Urea
    • 

  • Secondary alcohol
    • 

  • Ketimine
    • 

  • Ketone
    • 

  • Lactam
    • 

  • Organic 1,3-dipolar compound
    • 

  • Propargyl-type 1,3-dipolar organic compound
    • 

  • Secondary amine
    • 

  • Azacycle
    • 

  • Organic nitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • Imine
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
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-0.93ALOGPS
logP-1.1ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)8.27ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area119.89 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity65.52 m³·mol⁻¹ChemAxon
Polarizability21.77 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC02333  
BioCyc IDCPD-1127  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound439706  
PDB IDNot Available
ChEBI ID17953  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]