NP-MRD: Showing NP-Card for Glycocitrine II (NP0083533)

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Record Information

Version

2.0

Created at

2022-04-29 04:32:58 UTC

Updated at

2022-04-29 04:32:58 UTC

NP-MRD ID

NP0083533

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Glycocitrine II

Description

Glycocitrine II belongs to the class of organic compounds known as acridones. These are acridines containing a ketone group attached to the C9 carbon atom of the acridine moiety. Glycocitrine II is found in Glycosmis citrifolia and Glycosmis parviflora. Glycocitrine II is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 42 44  0  0  0  0  0  0  0  0999 V2000
   -4.4410   -0.3750   -1.2217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9470   -0.3335    0.1766 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9528   -0.2704    1.2753 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6598   -0.3520    0.4092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5508   -0.4104   -0.5676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5466    0.6337   -0.4885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9182    1.9621   -0.8295 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2957    2.1482   -1.1314 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0490    2.9894   -0.8706 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2811    2.7680   -0.5723 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1034    3.8469   -0.6335 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6983    1.5038   -0.2368 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0275    1.2489    0.0267 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8580    2.2075   -0.0107 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4497   -0.0055    0.3227 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7732   -0.2607    0.5547 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2297   -1.5381    0.8298 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3296   -2.5613    0.8674 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9670   -2.3189    0.6325 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5438   -1.0206    0.3621 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2009   -0.8216    0.1133 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2833   -1.9002    0.2997 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7690    0.4126   -0.1880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5073   -0.7497   -1.1940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5002    0.6293   -1.6630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8411   -1.0427   -1.8837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5783   -0.9939    2.0558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0385    0.7197    1.7344 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9467   -0.6403    0.9505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3671   -0.3114    1.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1798    0.0206   -1.4776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3933   -1.3313   -1.1161 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6178    3.0715   -1.3805 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3682    3.9807   -1.1314 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0188    4.0004   -0.4880 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4759    0.5603    0.5210 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2691   -1.7655    1.0171 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6197   -3.5987    1.0778 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2943   -3.1629    0.6380 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2363   -2.7044   -0.4075 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8343   -2.5080    1.1533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5639   -1.7264    0.9980 H   0  0  0  0  0  0  0  0  0  0  0  0
 22 21  1  0
 21 20  1  0
 20 19  2  0
 19 18  1  0
 18 17  2  0
 17 16  1  0
 16 15  2  0
 15 13  1  0
 13 14  2  0
 13 12  1  0
 12 10  2  0
 10 11  1  0
 10  9  1  0
  9  7  2  0
  7  8  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  2  2  3
  2  1  1  0
  2  3  1  0
  6 23  2  0
 23 21  1  0
 15 20  1  0
 23 12  1  0
 22 40  1  0
 22 41  1  0
 22 42  1  0
 19 39  1  0
 18 38  1  0
 17 37  1  0
 16 36  1  0
 11 35  1  0
  9 34  1  0
  8 33  1  0
  5 31  1  0
  5 32  1  0
  4 30  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  3 27  1  0
  3 28  1  0
  3 29  1  0
M  END


  Mrv1533004261504362D          

 23 25  0  0  0  0            999 V2000
    2.1434    2.0625    0.0000 C   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
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   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
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    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
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    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
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   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
  3  4  2  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
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 17 23  2  0  0  0  0
  2 23  1  0  0  0  0
 11 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0083533

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C2=CC=CC=C2C(=O)C2=C(O)C=C(O)C(CC=C(C)C)=C12

> <INCHI_IDENTIFIER>
InChI=1S/C19H19NO3/c1-11(2)8-9-13-15(21)10-16(22)17-18(13)20(3)14-7-5-4-6-12(14)19(17)23/h4-8,10,21-22H,9H2,1-3H3

> <INCHI_KEY>
ZVEGIYHOVGYFQS-UHFFFAOYSA-N

> <FORMULA>
C19H19NO3

> <MOLECULAR_WEIGHT>
309.365

> <EXACT_MASS>
309.136493476

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
33.057525200101516

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,3-dihydroxy-10-methyl-4-(3-methylbut-2-en-1-yl)-9,10-dihydroacridin-9-one

> <ALOGPS_LOGP>
3.46

> <JCHEM_LOGP>
4.894391234333334

> <ALOGPS_LOGS>
-3.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.609994859952554

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.872243201707095

> <JCHEM_PKA_STRONGEST_BASIC>
-1.1607442801762775

> <JCHEM_POLAR_SURFACE_AREA>
60.77000000000001

> <JCHEM_REFRACTIVITY>
92.163

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.08e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,3-dihydroxy-10-methyl-4-(3-methylbut-2-en-1-yl)acridin-9-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-APR-15         0                                  
HETATM    1  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       4.001   2.310   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   23                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3    9                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   23                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   23                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   17    2   11                                                  
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₁₉NO₃

Average Mass

309.3650 Da

Monoisotopic Mass

309.13649 Da

IUPAC Name

1,3-dihydroxy-10-methyl-4-(3-methylbut-2-en-1-yl)-9,10-dihydroacridin-9-one

Traditional Name

1,3-dihydroxy-10-methyl-4-(3-methylbut-2-en-1-yl)acridin-9-one

CAS Registry Number

Not Available

SMILES

CN1C2=CC=CC=C2C(=O)C2=C(O)C=C(O)C(CC=C(C)C)=C12

InChI Identifier

InChI=1S/C19H19NO3/c1-11(2)8-9-13-15(21)10-16(22)17-18(13)20(3)14-7-5-4-6-12(14)19(17)23/h4-8,10,21-22H,9H2,1-3H3

InChI Key

ZVEGIYHOVGYFQS-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 citrifolia	Plant	KNApSAcK
Glycosmis parviflora	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as acridones. These are acridines containing a ketone group attached to the C9 carbon atom of the acridine moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Quinolines and derivatives

Sub Class

Benzoquinolines

Direct Parent

Acridones

Alternative Parents

Substituents

Acridone
Dihydroquinolone
Dihydroquinoline
1-hydroxy-2-unsubstituted benzenoid
Phenol
Benzenoid
Pyridine
Heteroaromatic compound
Vinylogous amide
Vinylogous acid
Azacycle
Organic nitrogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Organic oxygen compound
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	3.46	ALOGPS
logP	4.89	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	7.87	ChemAxon
pKa (Strongest Basic)	-1.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	60.77 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	92.16 m³·mol⁻¹	ChemAxon
Polarizability	33.06 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11781835

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Glycocitrine II (NP0083533)

MOL for NP0083533 (Glycocitrine II)

3D MOL for NP0083533 (Glycocitrine II)

3D SDF for NP0083533 (Glycocitrine II)

3D-SDF for NP0083533 (Glycocitrine II)

PDB for NP0083533 (Glycocitrine II)

3D PDB for NP0083533 (Glycocitrine II)

SMILES for NP0083533 (Glycocitrine II)

INCHI for NP0083533 (Glycocitrine II)

Structure for NP0083533 (Glycocitrine II)

3D Structure for NP0083533 (Glycocitrine II)