NP-MRD: Showing NP-Card for Padmatin (NP0055868)

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Record Information

Version

2.0

Created at

2022-04-28 01:48:04 UTC

Updated at

2022-04-28 01:48:04 UTC

NP-MRD ID

NP0055868

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Padmatin

Description

(2R)-2,3-Dihydro-2alpha-(3,4-dihydroxyphenyl)-3alpha,5-dihydroxy-7-methoxy-4H-1-benzopyran-4-one belongs to the class of organic compounds known as 7-o-methylated flavonoids. These are flavonoids with methoxy groups attached to the C7 atom of the flavonoid backbone. Padmatin is found in Artemisia campestris , Artemisia glutinosa, Dittrichia graveolens, Inula viscosa , Pulicaria undulata , Inula graveolens, Prunus puddum and Trixis vanthrei. Based on a literature review very few articles have been published on (2R)-2,3-Dihydro-2alpha-(3,4-dihydroxyphenyl)-3alpha,5-dihydroxy-7-methoxy-4H-1-benzopyran-4-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 39  0  0  0  0  0  0  0  0999 V2000
    5.1943    2.7669    0.2582 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0050    2.6701   -0.5039 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2099    1.5193   -0.3510 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5655    0.5100    0.5101 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7425   -0.5886    0.6119 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0227   -1.6548    1.4557 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5703   -0.6850   -0.1387 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1993    0.3192   -1.0073 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0429    1.4167   -1.0943 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0343    0.2257   -1.7546 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9320   -0.7804   -1.6287 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0982   -0.3602   -0.7910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9194    0.3095    0.3995 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9834    0.7033    1.1835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3029    0.4409    0.8067 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3466    0.8546    1.6250 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4752   -0.2280   -0.3829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7734   -0.5048   -0.7871 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3950   -0.6248   -1.1733 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2958   -2.0455   -1.1404 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2328   -3.0233   -0.8108 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6833   -1.8337   -0.0496 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7423   -2.6127    0.9076 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8560    3.5656   -0.1049 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9418    2.9316    1.3206 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7679    1.8090    0.1015 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4643    0.5868    1.0839 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8706   -1.5952    2.0048 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8123    2.2437   -1.7579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2876   -1.0128   -2.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9082    0.5308    0.7238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8556    1.2316    2.1237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3165    0.6990    1.4152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6111   -0.2794   -0.3219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5643   -1.1475   -2.1005 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2849   -2.4775   -2.0077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7119   -3.8802   -0.7385 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  9  2  0
  9  8  1  0
  8  7  2  0
  7  5  1  0
  5  6  1  0
  5  4  2  0
  7 22  1  0
 22 23  2  0
 22 20  1  0
 20 21  1  0
 20 11  1  0
 11 10  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17 19  2  0
  4  3  1  0
 19 12  1  0
 10  8  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
  9 29  1  0
  6 28  1  0
  4 27  1  0
 20 36  1  6
 21 37  1  0
 11 30  1  6
 13 31  1  0
 14 32  1  0
 16 33  1  0
 18 34  1  0
 19 35  1  0
M  END


  Mrv1652304282203482D          

 23 25  0  0  1  0            999 V2000
   -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
   -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 O   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
    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  1  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   -1.6500    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
    0.0000   -2.4750    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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  3 12  1  0  0  0  0
 12 13  2  0  0  0  0
 11 14  1  6  0  0  0
 10 15  1  6  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 15 20  1  0  0  0  0
 19 21  1  0  0  0  0
 18 22  1  0  0  0  0
  2 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0055868

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC2=C(C(O)=C1)C(=O)[C@@H](O)[C@H](O2)C1=CC=C(O)C(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C16H14O7/c1-22-8-5-11(19)13-12(6-8)23-16(15(21)14(13)20)7-2-3-9(17)10(18)4-7/h2-6,15-19,21H,1H3/t15-,16-/m1/s1

> <INCHI_KEY>
MRPJBTFHICBFNE-HZPDHXFCSA-N

> <FORMULA>
C16H14O7

> <MOLECULAR_WEIGHT>
318.281

> <EXACT_MASS>
318.073952791

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
30.30314195549027

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3S)-2-(3,4-dihydroxyphenyl)-3,5-dihydroxy-7-methoxy-3,4-dihydro-2H-1-benzopyran-4-one

> <ALOGPS_LOGP>
1.33

> <JCHEM_LOGP>
1.9622783239999992

> <ALOGPS_LOGS>
-2.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.295424618692415

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.47604277359219

> <JCHEM_PKA_STRONGEST_BASIC>
-4.041177743066354

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
79.09120000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.24e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S)-2-(3,4-dihydroxyphenyl)-3,5-dihydroxy-7-methoxy-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  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -0.770   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  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   23                                                  
CONECT    3    2    4   12                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    4   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12   14                                                  
CONECT   12   11    3   13                                                  
CONECT   13   12                                                            
CONECT   14   11                                                            
CONECT   15   10   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   22                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19   15                                                       
CONECT   21   19                                                            
CONECT   22   18                                                            
CONECT   23    2                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

View in JSmol

Synonyms

Value	Source
(2R)-2,3-Dihydro-2a-(3,4-dihydroxyphenyl)-3a,5-dihydroxy-7-methoxy-4H-1-benzopyran-4-one	Generator
(2R)-2,3-Dihydro-2α-(3,4-dihydroxyphenyl)-3α,5-dihydroxy-7-methoxy-4H-1-benzopyran-4-one	Generator

Chemical Formula

C₁₆H₁₄O₇

Average Mass

318.2810 Da

Monoisotopic Mass

318.07395 Da

IUPAC Name

(2R,3S)-2-(3,4-dihydroxyphenyl)-3,5-dihydroxy-7-methoxy-3,4-dihydro-2H-1-benzopyran-4-one

Traditional Name

(2R,3S)-2-(3,4-dihydroxyphenyl)-3,5-dihydroxy-7-methoxy-2,3-dihydro-1-benzopyran-4-one

CAS Registry Number

Not Available

SMILES

COC1=CC2=C(C(O)=C1)C(=O)[C@@H](O)[C@H](O2)C1=CC=C(O)C(O)=C1

InChI Identifier

InChI=1S/C16H14O7/c1-22-8-5-11(19)13-12(6-8)23-16(15(21)14(13)20)7-2-3-9(17)10(18)4-7/h2-6,15-19,21H,1H3/t15-,16-/m1/s1

InChI Key

MRPJBTFHICBFNE-HZPDHXFCSA-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
Artemisia campestris	Plant	KNApSAcK
Artemisia glutinosa	Plant	KNApSAcK
Dittrichia graveolens	LOTUS Database	35616633
Dittrichia viscosa	Plant	KNApSAcK
Francoeuria undulata	Plant	KNApSAcK
Inula graveolens	Plant	KNApSAcK
Prunus puddum	Plant	KNApSAcK
Trixis vanthrei	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 7-o-methylated flavonoids. These are flavonoids with methoxy groups attached to the C7 atom of the flavonoid backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

O-methylated flavonoids

Direct Parent

7-O-methylated flavonoids

Alternative Parents

Substituents

7-methoxyflavonoid-skeleton
3'-hydroxyflavonoid
3-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
Flavanone
Flavanonol
Hydroxyflavonoid
Flavan
Chromone
Chromane
Benzopyran
1-benzopyran
Anisole
Catechol
Aryl alkyl ketone
Aryl ketone
Phenol
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Alkyl aryl ether
Benzenoid
Monocyclic benzene moiety
Vinylogous acid
Ketone
Secondary alcohol
Ether
Organoheterocyclic compound
Oxacycle
Organic oxide
Aldehyde
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Organooxygen 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	1.33	ALOGPS
logP	1.96	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	8.48	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.45 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	79.09 m³·mol⁻¹	ChemAxon
Polarizability	30.3 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

9647434

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11472604

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Padmatin (NP0055868)

MOL for NP0055868 (Padmatin)

3D MOL for NP0055868 (Padmatin)

3D SDF for NP0055868 (Padmatin)

3D-SDF for NP0055868 (Padmatin)

PDB for NP0055868 (Padmatin)

3D PDB for NP0055868 (Padmatin)

SMILES for NP0055868 (Padmatin)

INCHI for NP0055868 (Padmatin)

Structure for NP0055868 (Padmatin)

3D Structure for NP0055868 (Padmatin)