NP-MRD: Showing NP-Card for Calodenin B (NP0054391)

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Record Information

Version

1.0

Created at

2022-04-28 00:45:24 UTC

Updated at

2022-04-28 00:45:24 UTC

NP-MRD ID

NP0054391

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Calodenin B

Description

Calodenin B belongs to the class of organic compounds known as 2-arylbenzofuran flavonoids. These are phenylpropanoids containing the 2-phenylbenzofuran moiety. Calodenin B is found in Brackenridgea zanguebarica , Cordia goetzei, Ochna afzelii , Ochna calodendron and Ochna integerrima. It was first documented in 2003 (PMID: 12677529). Based on a literature review a small amount of articles have been published on Calodenin B (PMID: 33582268) (PMID: 16872561).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282202452D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282202452D          

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M  END
> <DATABASE_ID>
NP0054391

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC=C(\C=C\C(=O)C2=C3OC(=C(C(=O)C4=C(O)C=C(O)C=C4)C3=C(O)C=C2O)C2=CC=C(O)C=C2)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H20O9/c31-17-6-1-15(2-7-17)3-12-21(34)25-23(36)14-24(37)26-27(28(38)20-11-10-19(33)13-22(20)35)29(39-30(25)26)16-4-8-18(32)9-5-16/h1-14,31-33,35-37H/b12-3+

> <INCHI_KEY>
OYSSHUWICGHBOU-KGVSQERTSA-N

> <FORMULA>
C30H20O9

> <MOLECULAR_WEIGHT>
524.481

> <EXACT_MASS>
524.110732224

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
52.60605396382876

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2E)-1-[3-(2,4-dihydroxybenzoyl)-4,6-dihydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-yl]-3-(4-hydroxyphenyl)prop-2-en-1-one

> <ALOGPS_LOGP>
4.51

> <JCHEM_LOGP>
6.554636302666665

> <ALOGPS_LOGS>
-4.05

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.9751966367334814

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.211036254346736

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9456456921342125

> <JCHEM_POLAR_SURFACE_AREA>
168.66

> <JCHEM_REFRACTIVITY>
143.19269999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.67e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2E)-1-[3-(2,4-dihydroxybenzoyl)-4,6-dihydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-yl]-3-(4-hydroxyphenyl)prop-2-en-1-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  O   UNK     0       6.121   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       3.322  -0.476   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.877   0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.107  -0.564   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.433  -0.564   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.203   0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.433   2.104   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.107   2.104   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -3.743   0.770   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.846   3.481   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       1.340   3.801   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       3.877   4.625   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.401   6.090   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.432   7.234   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.938   6.914   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.414   5.449   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.383   4.305   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       6.968   8.058   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       1.895   6.410   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       6.121  -2.310   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       4.787  -3.080   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       7.454  -3.080   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.788  -2.310   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.122  -3.080   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      11.455  -2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      12.789  -3.080   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      12.789  -4.620   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      11.455  -5.390   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      10.122  -4.620   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      14.123  -5.390   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       8.788  -0.770   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   39                                                  
CONECT    5    4    6   28                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    2    8                                                  
CONECT    8    7    9   18                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9    6                                                       
CONECT   11    9   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15   11                                                       
CONECT   17   14                                                            
CONECT   18    8   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   25                                                  
CONECT   21   20   22   27                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24   20                                                       
CONECT   26   23                                                            
CONECT   27   21                                                            
CONECT   28    5   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   37                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36   38                                                  
CONECT   36   35   37                                                       
CONECT   37   36   32                                                       
CONECT   38   35                                                            
CONECT   39    4                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₂₀O₉

Average Mass

524.4810 Da

Monoisotopic Mass

524.11073 Da

IUPAC Name

(2E)-1-[3-(2,4-dihydroxybenzoyl)-4,6-dihydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-yl]-3-(4-hydroxyphenyl)prop-2-en-1-one

Traditional Name

(2E)-1-[3-(2,4-dihydroxybenzoyl)-4,6-dihydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-yl]-3-(4-hydroxyphenyl)prop-2-en-1-one

CAS Registry Number

Not Available

SMILES

OC1=CC=C(\C=C\C(=O)C2=C3OC(=C(C(=O)C4=C(O)C=C(O)C=C4)C3=C(O)C=C2O)C2=CC=C(O)C=C2)C=C1

InChI Identifier

InChI=1S/C30H20O9/c31-17-6-1-15(2-7-17)3-12-21(34)25-23(36)14-24(37)26-27(28(38)20-11-10-19(33)13-22(20)35)29(39-30(25)26)16-4-8-18(32)9-5-16/h1-14,31-33,35-37H/b12-3+

InChI Key

OYSSHUWICGHBOU-KGVSQERTSA-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
Brackenridgea zanguebarica	Plant	KNApSAcK
Cordia goetzei	Plant	KNApSAcK
Ochna afzelii	Plant	KNApSAcK
Ochna calodendron	Plant	KNApSAcK
Ochna integerrima	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2-arylbenzofuran flavonoids. These are phenylpropanoids containing the 2-phenylbenzofuran moiety.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

2-arylbenzofuran flavonoids

Sub Class

Not Available

Direct Parent

2-arylbenzofuran flavonoids

Alternative Parents

Substituents

2-arylbenzofuran flavonoid
2'-hydroxychalcone
2-phenylbenzofuran
Phenylbenzofuran
Aryl-phenylketone
Cinnamic acid or derivatives
Hydroxycinnamic acid or derivatives
Benzofuran
Benzoyl
Aryl ketone
3-aroylfuran
Styrene
Resorcinol
Phenol
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Monocyclic benzene moiety
Benzenoid
Acryloyl-group
Heteroaromatic compound
Enone
Furan
Vinylogous acid
Alpha,beta-unsaturated ketone
Ketone
Oxacycle
Organoheterocyclic compound
Organic oxide
Organooxygen compound
Hydrocarbon derivative
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	4.51	ALOGPS
logP	6.55	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	6.21	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	168.66 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	143.19 m³·mol⁻¹	ChemAxon
Polarizability	52.61 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00006551

Chemspider ID

8182600

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10007020

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kalenga TM, Ndoile MM, Atilaw Y, Munissi JJE, Gilissen PJ, Rudenko A, Bourgard C, Sunnerhagen P, Nyandoro SS, Erdelyi M: Antibacterial and cytotoxic biflavonoids from the root bark of Ochna kirkii. Fitoterapia. 2021 Jun;151:104857. doi: 10.1016/j.fitote.2021.104857. Epub 2021 Feb 11. [PubMed:33582268 ]
Moller M, Suschke U, Nolkemper S, Schneele J, Distl M, Sporer F, Reichling J, Wink M: Antibacterial, antiviral, antiproliferative and apoptosis-inducing properties of Brackenridgea zanguebarica (Ochnaceae). J Pharm Pharmacol. 2006 Aug;58(8):1131-8. doi: 10.1211/jpp.58.8.0015. [PubMed:16872561 ]
Tang S, Bremner P, Kortenkamp A, Schlage C, Gray AI, Gibbons S, Heinrich M: Biflavonoids with cytotoxic and antibacterial activity from Ochna macrocalyx. Planta Med. 2003 Mar;69(3):247-53. doi: 10.1055/s-2003-38478. [PubMed:12677529 ]

Showing NP-Card for Calodenin B (NP0054391)

MOL for NP0054391 (Calodenin B)

3D MOL for NP0054391 (Calodenin B)

3D SDF for NP0054391 (Calodenin B)

3D-SDF for NP0054391 (Calodenin B)

PDB for NP0054391 (Calodenin B)

3D PDB for NP0054391 (Calodenin B)

SMILES for NP0054391 (Calodenin B)

INCHI for NP0054391 (Calodenin B)

Structure for NP0054391 (Calodenin B)

3D Structure for NP0054391 (Calodenin B)