NP-MRD: Showing NP-Card for Pulchellidin (NP0054450)

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Record Information

Version

2.0

Created at

2022-04-28 00:48:11 UTC

Updated at

2022-04-28 00:48:11 UTC

NP-MRD ID

NP0054450

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pulchellidin

Description

[3,7-Dihydroxy-2-(3,4,5-trihydroxyphenyl)-5H-chromen-5-ylidene](methyl)oxidanium belongs to the class of organic compounds known as 5-o-methylated flavonoids. These are flavonoids with methoxy groups attached to the C5 atom of the flavonoid backbone. Pulchellidin is found in Plumbago pulchella. [3,7-Dihydroxy-2-(3,4,5-trihydroxyphenyl)-5H-chromen-5-ylidene](methyl)oxidanium is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 38  0  0  0  0  0  0  0  0999 V2000
   -5.4238    1.7186   -0.5967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0181    1.5188   -0.6001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4191    0.4546    0.0523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1291   -0.4830    0.7474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4343   -1.5165    1.3699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2060   -2.4447    2.0648 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0650   -1.6015    1.2935 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3349   -0.6531    0.5892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0410   -0.7128    0.5032 O   0  0  0  0  0  3  0  0  0  0  0  0
    0.7149    0.1716   -0.1609 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1485   -0.0002   -0.1856 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0695    0.7872   -0.8009 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4429    0.5408   -0.7700 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2544    1.4353   -1.4462 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9172   -0.5365   -0.0969 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2709   -0.8001   -0.0526 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0255   -1.3745    0.5493 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5571   -2.4616    1.2234 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6814   -1.1092    0.5029 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0719    1.1937   -0.7808 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7424    2.1620   -1.4926 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3266    1.2914   -0.7100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0438    0.3512   -0.0124 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6628    2.6960   -1.0253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7284    1.7626    0.4793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8773    0.8618   -1.1027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1950   -0.4351    0.8191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8231   -3.2337    2.5544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5553   -2.4137    1.7863 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7417    1.6422   -1.3399 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2575    1.3458   -1.4840 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9861   -0.2521   -0.4880 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9856   -3.1327    1.7270 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0099   -1.7800    1.0161 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2335    2.9045   -1.9388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8272    2.1028   -1.2031 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3 23  2  0
 23 22  1  0
 22 20  2  0
 20 21  1  0
 20 10  1  0
 10  9  2  0
  9  8  1  0
  8  7  2  0
  7  5  1  0
  5  6  1  0
  5  4  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 13 15  2  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17 19  2  0
  4  3  1  0
 19 11  1  0
  8 23  1  0
  1 24  1  0
  1 25  1  0
  1 26  1  0
 22 36  1  0
 21 35  1  0
  7 29  1  0
  6 28  1  0
  4 27  1  0
 12 30  1  0
 14 31  1  0
 16 32  1  0
 18 33  1  0
 19 34  1  0
M  CHG  1   9   1
M  END


  Mrv1533004191515242D          

 23 25  0  0  0  0            999 V2000
    0.7145   -2.8875    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
    1.4289   -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 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
    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  3  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
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    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
    4.2868   -0.0000    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
    5.0013    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    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  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
 13 14  1  0  0  0  0
  3 14  2  0  0  0  0
  8 14  1  0  0  0  0
 10 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  2  0  0  0  0
 15 23  1  0  0  0  0
M  CHG  1   9   1
M  END
> <DATABASE_ID>
NP0054450

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C2C=C(O)C(=[O+]C2=CC(O)=C1)C1=CC(O)=C(O)C(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C16H12O7/c1-22-13-4-8(17)5-14-9(13)6-12(20)16(23-14)7-2-10(18)15(21)11(19)3-7/h2-6H,1H3,(H4-,17,18,19,20,21)/p+1

> <INCHI_KEY>
SVUQABVHSHQZHD-UHFFFAOYSA-O

> <FORMULA>
C16H13O7

> <MOLECULAR_WEIGHT>
317.272

> <EXACT_MASS>
317.065579179

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
31.039823324433307

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3,7-dihydroxy-5-methoxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium

> <ALOGPS_LOGP>
2.51

> <JCHEM_LOGP>
2.797599999999999

> <ALOGPS_LOGS>
-3.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.986059536441691

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.056098465116737

> <JCHEM_PKA_STRONGEST_BASIC>
-4.8977454869563015

> <JCHEM_POLAR_SURFACE_AREA>
123.52000000000001

> <JCHEM_REFRACTIVITY>
90.57629999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.12e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pulchellidin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.667  -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  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+1
HETATM   10  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      12.003   2.310   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      12.003  -0.770   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   14                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    3    8                                                  
CONECT   15   10   16   23                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   15                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₁₃O₇

Average Mass

317.2720 Da

Monoisotopic Mass

317.06558 Da

IUPAC Name

3,7-dihydroxy-5-methoxy-2-(3,4,5-trihydroxyphenyl)-1λ⁴-chromen-1-ylium

Traditional Name

pulchellidin

CAS Registry Number

Not Available

SMILES

COC1=C2C=C(O)C(=[O+]C2=CC(O)=C1)C1=CC(O)=C(O)C(O)=C1

InChI Identifier

InChI=1S/C16H12O7/c1-22-13-4-8(17)5-14-9(13)6-12(20)16(23-14)7-2-10(18)15(21)11(19)3-7/h2-6H,1H3,(H4-,17,18,19,20,21)/p+1

InChI Key

SVUQABVHSHQZHD-UHFFFAOYSA-O

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
Plumbago pulchella	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5-o-methylated flavonoids. These are flavonoids with methoxy groups attached to the C5 atom of the flavonoid backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

O-methylated flavonoids

Direct Parent

5-O-methylated flavonoids

Alternative Parents

Substituents

5-methoxyflavonoid-skeleton
Hydroxyflavonoid
3'-hydroxyflavonoid
3-hydroxyflavonoid
4'-hydroxyflavonoid
7-hydroxyflavonoid
Anthocyanidin
Benzopyran
1-benzopyran
Benzenetriol
Pyrogallol derivative
Phenol ether
Anisole
1-hydroxy-4-unsubstituted benzenoid
Alkyl aryl ether
Phenol
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Monocyclic benzene moiety
Heteroaromatic compound
Polyol
Organoheterocyclic compound
Oxacycle
Ether
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
Organic cation
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	2.51	ALOGPS
logP	2.8	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	6.06	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	123.52 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	90.58 m³·mol⁻¹	ChemAxon
Polarizability	31.04 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

14496545

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Pulchellidin (NP0054450)

MOL for NP0054450 (Pulchellidin)

3D MOL for NP0054450 (Pulchellidin)

3D SDF for NP0054450 (Pulchellidin)

3D-SDF for NP0054450 (Pulchellidin)

PDB for NP0054450 (Pulchellidin)

3D PDB for NP0054450 (Pulchellidin)

SMILES for NP0054450 (Pulchellidin)

INCHI for NP0054450 (Pulchellidin)

Structure for NP0054450 (Pulchellidin)

3D Structure for NP0054450 (Pulchellidin)