NP-MRD: Showing NP-Card for Plathymenin (NP0055612)

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Record Information

Version

2.0

Created at

2022-04-28 01:36:34 UTC

Updated at

2022-04-28 01:36:35 UTC

NP-MRD ID

NP0055612

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Plathymenin

Description

Plathymenin belongs to the class of organic compounds known as flavanones. Flavanones are compounds containing a flavan-3-one moiety, with a structure characterized by a 2-phenyl-3,4-dihydro-2H-1-benzopyran bearing a ketone at the carbon C3. Plathymenin is found in Dalbergia sissoo, Plathymenia reticulata and Spatholobus suberectus Dunn . Plathymenin was first documented in 2006 (PMID: 16782143). Based on a literature review a small amount of articles have been published on Plathymenin (PMID: 25614224) (PMID: 26024248).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 35  0  0  0  0  0  0  0  0999 V2000
    0.3300   -2.8826    1.1722 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4952   -2.2181    0.1144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1290   -2.5797   -1.1773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5158   -1.2946   -1.8710 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4027   -0.5300   -0.9492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1536   -1.1107    0.0491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9766   -0.3838    0.9101 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0518    0.9803    0.7668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8748    1.6816    1.6324 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3136    1.5899   -0.2213 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4306    2.9771   -0.3187 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5030    0.8649   -1.0678 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7284   -0.5992   -2.0732 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4539   -0.2268   -0.9445 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2522    0.9139   -0.9460 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9660    1.2721    0.1787 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7689    2.4289    0.1610 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8602    0.4662    1.2931 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5372    0.7570    2.4430 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0560   -0.6746    1.2804 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3408   -1.0361    0.1579 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6981   -3.0108   -1.7953 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9706   -3.2934   -1.0798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9803   -1.4646   -2.8575 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1133   -2.1955    0.1788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5251   -0.9368    1.6615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4161    1.2352    2.3570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9040    3.4367   -1.0278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9326    1.3595   -1.8354 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3021    1.5141   -1.8459 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3112    2.7408    0.9480 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1338    1.5381    2.5633 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9595   -1.3194    2.1432 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8  7  2  0
  7  6  1  0
  6  5  2  0
  5 12  1  0
 12 10  2  0
 10 11  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  0
  2 21  1  0
 21 20  2  0
 20 18  1  0
 18 19  1  0
 18 16  2  0
 16 17  1  0
 16 15  1  0
 15 14  2  0
 14 13  1  0
 10  8  1  0
 13  4  1  0
 14 21  1  0
  9 27  1  0
  7 26  1  0
  6 25  1  0
 12 29  1  0
 11 28  1  0
  4 24  1  6
  3 22  1  0
  3 23  1  0
 20 33  1  0
 19 32  1  0
 17 31  1  0
 15 30  1  0
M  END


  Mrv1652304282203362D          

 21 23  0  0  1  0            999 V2000
   -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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  1  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
    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
    2.8579   -0.0000    0.0000 C   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
    5.0013   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  2  0  0  0  0
  8 12  1  6  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 12 17  1  0  0  0  0
 16 18  1  0  0  0  0
 15 19  1  0  0  0  0
  2 20  1  0  0  0  0
  1 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0055612

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC=C(C=C1O)[C@@H]1CC(=O)C2=CC(O)=C(O)C=C2O1

> <INCHI_IDENTIFIER>
InChI=1S/C15H12O6/c16-9-2-1-7(3-11(9)18)14-5-10(17)8-4-12(19)13(20)6-15(8)21-14/h1-4,6,14,16,18-20H,5H2/t14-/m0/s1

> <INCHI_KEY>
ZIKILYZOICUSQT-AWEZNQCLSA-N

> <FORMULA>
C15H12O6

> <MOLECULAR_WEIGHT>
288.255

> <EXACT_MASS>
288.063388106

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
27.392964837296006

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-2-(3,4-dihydroxyphenyl)-6,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-4-one

> <ALOGPS_LOGP>
2.14

> <JCHEM_LOGP>
1.8815427286666666

> <ALOGPS_LOGS>
-3.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.232255187105789

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.871500478908681

> <JCHEM_PKA_STRONGEST_BASIC>
-4.925034057425487

> <JCHEM_POLAR_SURFACE_AREA>
107.22000000000001

> <JCHEM_REFRACTIVITY>
73.27070000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.86e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-(3,4-dihydroxyphenyl)-6,7-dihydroxy-2,3-dihydro-1-benzopyran-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    6   21                                                  
CONECT    2    1    3   20                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10                                                       
CONECT   10    9    4   11                                                  
CONECT   11   10                                                            
CONECT   12    8   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   19                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16   12                                                       
CONECT   18   16                                                            
CONECT   19   15                                                            
CONECT   20    2                                                            
CONECT   21    1                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₁₂O₆

Average Mass

288.2550 Da

Monoisotopic Mass

288.06339 Da

IUPAC Name

(2S)-2-(3,4-dihydroxyphenyl)-6,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-4-one

Traditional Name

(2S)-2-(3,4-dihydroxyphenyl)-6,7-dihydroxy-2,3-dihydro-1-benzopyran-4-one

CAS Registry Number

Not Available

SMILES

OC1=CC=C(C=C1O)[C@@H]1CC(=O)C2=CC(O)=C(O)C=C2O1

InChI Identifier

InChI=1S/C15H12O6/c16-9-2-1-7(3-11(9)18)14-5-10(17)8-4-12(19)13(20)6-15(8)21-14/h1-4,6,14,16,18-20H,5H2/t14-/m0/s1

InChI Key

ZIKILYZOICUSQT-AWEZNQCLSA-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
Dalbergia sissoo	LOTUS Database	35616633
Plathymenia reticulata	Plant	KNApSAcK
Spatholobus suberectus	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavanones. Flavanones are compounds containing a flavan-3-one moiety, with a structure characterized by a 2-phenyl-3,4-dihydro-2H-1-benzopyran bearing a ketone at the carbon C3.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavans

Direct Parent

Flavanones

Alternative Parents

Substituents

Flavanone
Hydroxyflavonoid
7-hydroxyflavonoid
6-hydroxyflavonoid
4'-hydroxyflavonoid
3'-hydroxyflavonoid
Chromone
1-benzopyran
Benzopyran
Chromane
Aryl alkyl ketone
Aryl ketone
Catechol
Alkyl aryl ether
Phenol
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Benzenoid
Monocyclic benzene moiety
Ketone
Organoheterocyclic compound
Oxacycle
Ether
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
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	2.14	ALOGPS
logP	1.88	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	7.87	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	107.22 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	73.27 m³·mol⁻¹	ChemAxon
Polarizability	27.39 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

C00006972

Chemspider ID

62907042

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

102196479

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Funakoshi-Tago M, Okamoto K, Izumi R, Tago K, Yanagisawa K, Narukawa Y, Kiuchi F, Kasahara T, Tamura H: Anti-inflammatory activity of flavonoids in Nepalese propolis is attributed to inhibition of the IL-33 signaling pathway. Int Immunopharmacol. 2015 Mar;25(1):189-98. doi: 10.1016/j.intimp.2015.01.012. Epub 2015 Jan 19. [PubMed:25614224 ]
Jiang S, Huang K, Liu W, Fu F, Xu J: Combined Autodock and comparative molecular field analysis study on predicting 5-lipoxygenase inhibitory activity of flavonoids isolated from Spatholobus suberectus Dunn. Z Naturforsch C J Biosci. 2015;70(3-4):103-13. doi: 10.1515/znc-2014-4110. [PubMed:26024248 ]
Lee MH, Lin YP, Hsu FL, Zhan GR, Yen KY: Bioactive constituents of Spatholobus suberectus in regulating tyrosinase-related proteins and mRNA in HEMn cells. Phytochemistry. 2006 Jun;67(12):1262-70. doi: 10.1016/j.phytochem.2006.05.008. Epub 2006 Jun 19. [PubMed:16782143 ]

Showing NP-Card for Plathymenin (NP0055612)

MOL for NP0055612 (Plathymenin)

3D MOL for NP0055612 (Plathymenin)

3D SDF for NP0055612 (Plathymenin)

3D-SDF for NP0055612 (Plathymenin)

PDB for NP0055612 (Plathymenin)

3D PDB for NP0055612 (Plathymenin)

SMILES for NP0055612 (Plathymenin)

INCHI for NP0055612 (Plathymenin)

Structure for NP0055612 (Plathymenin)

3D Structure for NP0055612 (Plathymenin)