NP-MRD: Showing NP-Card for Glycophymine (NP0051226)

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Record Information

Version

2.0

Created at

2022-04-27 22:37:16 UTC

Updated at

2022-04-27 22:37:16 UTC

NP-MRD ID

NP0051226

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Glycophymine

Description

Glycosminine, also known as glycophymine, belongs to the class of organic compounds known as quinazolines. Quinazolines are compounds containing a quinazoline moiety, which is made up of two fused six-member aromatic rings, a benzene ring and a pyrimidine ring. Glycophymine is found in Glycosmis arborea, Glycosmis pentaphylla and Ruta sp.. Glycosminine is a moderately basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 32  0  0  0  0  0  0  0  0999 V2000
   -1.5483    1.0386   -3.2027 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3555    0.4298   -2.1065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2428   -0.2680   -1.8612 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0905   -0.8905   -0.6894 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1205   -1.6697   -0.3798 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1850   -0.8861    0.2534 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1120   -0.2682   -0.5600 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1518    0.4924   -0.0448 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2668    0.6391    1.3348 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3478    0.0267    2.1448 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3244   -0.7230    1.6151 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0503   -0.8146    0.2349 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1985   -0.1356    0.0704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1722   -0.0746    1.0428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3369    0.6314    0.8386 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4824    1.2691   -0.3736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5160    1.2150   -1.3524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3379    0.5045   -1.1538 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5098   -0.3149   -2.6131 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5560   -2.1571   -1.2828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8461   -2.4929    0.3163 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0644   -0.3529   -1.6400 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8509    0.9567   -0.6941 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0666    1.2254    1.7580 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4740    0.1669    3.2232 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6232   -1.1890    2.2602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0485   -0.5779    1.9895 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1120    0.6851    1.6016 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3941    1.8224   -0.5347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6133    1.7118   -2.3149 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
  4 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18  2  1  0
 11  6  1  0
 18 13  1  0
  3 19  1  0
  5 20  1  0
  5 21  1  0
  7 22  1  0
  8 23  1  0
  9 24  1  0
 10 25  1  0
 11 26  1  0
 14 27  1  0
 15 28  1  0
 16 29  1  0
 17 30  1  0
M  END


  Mrv0541 05061306562D          

 18 20  0  0  0  0            999 V2000
   -6.5174   -1.3604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5174   -2.1854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2318   -2.5979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9463   -2.1854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9463   -1.3604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2318   -0.9479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2318   -0.1229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5174    0.2896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5174    1.1146    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8029    1.5271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0884    1.1146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3740    1.5271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6595    1.1146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6595    0.2896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3740   -0.1229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0884    0.2896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8029   -0.1229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8029    2.3521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  2  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 17  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 18  2  0  0  0  0
 11 12  2  0  0  0  0
 11 16  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0051226

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O=C1NC(CC2=CC=CC=C2)=NC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C15H12N2O/c18-15-12-8-4-5-9-13(12)16-14(17-15)10-11-6-2-1-3-7-11/h1-9H,10H2,(H,16,17,18)

> <INCHI_KEY>
ZDUVLDCZFKNYHH-UHFFFAOYSA-N

> <FORMULA>
C15H12N2O

> <MOLECULAR_WEIGHT>
236.2686

> <EXACT_MASS>
236.094963016

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
25.078563622763888

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-benzyl-3,4-dihydroquinazolin-4-one

> <ALOGPS_LOGP>
2.50

> <JCHEM_LOGP>
2.607780321

> <ALOGPS_LOGS>
-3.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.838551262632311

> <JCHEM_PKA_STRONGEST_BASIC>
2.7672104365902905

> <JCHEM_POLAR_SURFACE_AREA>
41.46

> <JCHEM_REFRACTIVITY>
72.1118

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.32e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-benzyl-3H-quinazolin-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

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     -12.166  -2.539   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -12.166  -4.079   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0     -13.499  -4.849   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -14.833  -4.079   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -14.833  -2.539   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -13.499  -1.769   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -13.499  -0.229   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -12.166   0.541   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0     -12.166   2.081   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0     -10.832   2.851   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -9.498   2.081   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -8.165   2.851   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.831   2.081   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.831   0.541   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -8.165  -0.229   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -9.498   0.541   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0     -10.832  -0.229   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0     -10.832   4.391   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    1    5    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   17                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   18                                                  
CONECT   11   10   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   11   15   17                                                  
CONECT   17    8   16                                                       
CONECT   18   10                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

View in JSmol

Synonyms

Value	Source
2-(Phenylmethyl)-4(3H)-quinazolinone, 9ci	HMDB
2-(Phenylmethyl)-4-quinoxalinol	HMDB
2-Benzyl-1H-quinazolin-4-one	HMDB
2-Benzyl-3H-quinazolin-4-one	HMDB
2-Benzyl-4-hydroxyquinazoline	HMDB
2-Benzylquinazolin-4(3H)-one	HMDB
2-Phenylmethyl-4(1H)-quinazolinone	HMDB
Glycophymine	HMDB
N-Demethylarborine	HMDB

Chemical Formula

C₁₅H₁₂N₂O

Average Mass

236.2686 Da

Monoisotopic Mass

236.09496 Da

IUPAC Name

2-benzyl-3,4-dihydroquinazolin-4-one

Traditional Name

2-benzyl-3H-quinazolin-4-one

CAS Registry Number

Not Available

SMILES

O=C1NC(CC2=CC=CC=C2)=NC2=CC=CC=C12

InChI Identifier

InChI=1S/C15H12N2O/c18-15-12-8-4-5-9-13(12)16-14(17-15)10-11-6-2-1-3-7-11/h1-9H,10H2,(H,16,17,18)

InChI Key

ZDUVLDCZFKNYHH-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Glycosmis arborea	Plant	KNApSAcK
Glycosmis pentaphylla	Plant	KNApSAcK
Ruta sp.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as quinazolines. Quinazolines are compounds containing a quinazoline moiety, which is made up of two fused six-member aromatic rings, a benzene ring and a pyrimidine ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazanaphthalenes

Sub Class

Benzodiazines

Direct Parent

Quinazolines

Alternative Parents

Substituents

Quinazoline
Pyrimidone
Monocyclic benzene moiety
Pyrimidine
Benzenoid
Vinylogous amide
Heteroaromatic compound
Azacycle
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

quinazolines (CHEBI:5497 )
Quinazoline alkaloids (C10688 )

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	2.5	ALOGPS
logP	2.61	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	9.84	ChemAxon
pKa (Strongest Basic)	2.77	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	41.46 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	72.11 m³·mol⁻¹	ChemAxon
Polarizability	25.08 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0033122

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

63121

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Glycophymine (NP0051226)

MOL for NP0051226 (Glycophymine)

3D MOL for NP0051226 (Glycophymine)

3D SDF for NP0051226 (Glycophymine)

3D-SDF for NP0051226 (Glycophymine)

PDB for NP0051226 (Glycophymine)

3D PDB for NP0051226 (Glycophymine)

SMILES for NP0051226 (Glycophymine)

INCHI for NP0051226 (Glycophymine)

Structure for NP0051226 (Glycophymine)

3D Structure for NP0051226 (Glycophymine)