NP-MRD: Showing NP-Card for cladophorol A (NP0333033)

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Record Information

Version

2.0

Created at

2024-05-03 14:16:53 UTC

Updated at

2025-02-11 15:44:11 UTC

NP-MRD ID

NP0333033

Natural Product DOI

https://doi.org/10.57994/2326

Secondary Accession Numbers

None

Natural Product Identification

Common Name

cladophorol A

Description

CHEMBL266458 belongs to the class of organic compounds known as 6,7-dihydroxycoumarins. These are coumarins bearing two hydroxyl groups at positions 6 and 7 of the coumarin skeleton, respectively. cladophorol A was first documented in 2019 (PMID: 30908914). CHEMBL266458 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652310051702132D          

 19 21  0  0  0  0            999 V2000
    3.4914   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3164   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0789   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4914   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3164   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6039   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0789   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7289    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5539   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2211   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4914   -2.9684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  2  0  0  0  0
  6  2  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  2  0  0  0  0
  7  5  1  0  0  0  0
  8  1  1  0  0  0  0
  9  2  2  0  0  0  0
 10  3  1  0  0  0  0
 10  8  2  0  0  0  0
 11  4  2  0  0  0  0
 11  9  1  0  0  0  0
 12  4  1  0  0  0  0
 12  6  2  0  0  0  0
 13  7  1  0  0  0  0
 14  8  1  0  0  0  0
 15  9  1  0  0  0  0
 16 10  1  0  0  0  0
 17 11  1  0  0  0  0
 18 13  2  0  0  0  0
 19 12  1  0  0  0  0
 19 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0333033

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC2=C(C=C1O)C1=CC(O)=C(O)C=C1C(=O)O2

> <INCHI_IDENTIFIER>
InChI=1S/C13H8O6/c14-8-1-5-6-2-9(15)11(17)4-12(6)19-13(18)7(5)3-10(8)16/h1-4,14-17H

> <INCHI_KEY>
OSFIGXJLZQHGJN-UHFFFAOYSA-N

> <FORMULA>
C13H8O6

> <MOLECULAR_WEIGHT>
260.201

> <EXACT_MASS>
260.032087978

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
24.157887277147488

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2,3,8,9-tetrahydroxy-6H-benzo[c]chromen-6-one

> <ALOGPS_LOGP>
1.87

> <JCHEM_LOGP>
1.7110661546666663

> <ALOGPS_LOGS>
-2.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.011568911980007

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.280680024726591

> <JCHEM_PKA_STRONGEST_BASIC>
-6.270073951394566

> <JCHEM_POLAR_SURFACE_AREA>
107.22000000000001

> <JCHEM_REFRACTIVITY>
64.86270000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.94e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3,8,9-tetrahydroxybenzo[c]chromen-6-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-OCT-17         0                                  
HETATM    1  C   UNK     0       6.517  -0.206   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.437  -0.206   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.057  -2.874   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.897  -2.874   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.747  -1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.207  -1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.517  -2.874   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.057  -0.206   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.897  -0.206   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.827  -1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.127  -1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.437  -2.874   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.747  -4.207   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.827   1.127   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.127   1.127   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      10.367  -1.540   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -0.413  -1.540   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       6.517  -5.541   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       4.207  -4.207   0.000  0.00  0.00           O+0
CONECT    1    5    8                                                       
CONECT    2    6    9                                                       
CONECT    3    7   10                                                       
CONECT    4   11   12                                                       
CONECT    5    1    6    7                                                  
CONECT    6    2    5   12                                                  
CONECT    7    3    5   13                                                  
CONECT    8    1   10   14                                                  
CONECT    9    2   11   15                                                  
CONECT   10    3    8   16                                                  
CONECT   11    4    9   17                                                  
CONECT   12    4    6   19                                                  
CONECT   13    7   18   19                                                  
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16   10                                                            
CONECT   17   11                                                            
CONECT   18   13                                                            
CONECT   19   12   13                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₈O₆

Average Mass

260.2010 Da

Monoisotopic Mass

260.03209 Da

IUPAC Name

2,3,8,9-tetrahydroxy-6H-benzo[c]chromen-6-one

Traditional Name

2,3,8,9-tetrahydroxybenzo[c]chromen-6-one

CAS Registry Number

Not Available

SMILES

OC1=CC2=C(C=C1O)C1=CC(O)=C(O)C=C1C(=O)O2

InChI Identifier

InChI=1S/C13H8O6/c14-8-1-5-6-2-9(15)11(17)4-12(6)19-13(18)7(5)3-10(8)16/h1-4,14-17H

InChI Key

OSFIGXJLZQHGJN-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 800 MHz, CD3OD, experimental)	serge_lavoie@uqac.ca	Not Available	Serge Lavoie	2024-05-03	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 800 MHz, CD3OD, experimental)	serge_lavoie@uqac.ca	Not Available	Serge Lavoie	2024-05-03	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 800 MHz, CD3OD, experimental)	serge_lavoie@uqac.ca	Not Available	Serge Lavoie	2024-05-03	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, CD3OD, experimental)	serge_lavoie@uqac.ca	Not Available	Serge Lavoie	2024-05-03	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, CD3OD, experimental)	serge_lavoie@uqac.ca	Not Available	Serge Lavoie	2024-05-03	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 800.23, CD₃OD, simulated)	serge_lavoie@uqac.ca	Université du Québec à Chicoutimi	Serge Lavoie	2024-05-03	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Cladophora socialis		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 6,7-dihydroxycoumarins. These are coumarins bearing two hydroxyl groups at positions 6 and 7 of the coumarin skeleton, respectively.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Hydroxycoumarins

Direct Parent

6,7-dihydroxycoumarins

Alternative Parents

Substituents

6,7-dihydroxycoumarin
Isocoumarin
Benzopyran
2-benzopyran
1-benzopyran
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Pyran
Benzenoid
Heteroaromatic compound
Lactone
Oxacycle
Polyol
Organoheterocyclic compound
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	1.87	ALOGPS
logP	1.71	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	7.28	ChemAxon
pKa (Strongest Basic)	-6.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	107.22 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	64.86 m³·mol⁻¹	ChemAxon
Polarizability	24.16 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

HMDB0145661

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

21255407

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

DOI: 10.1021/acs.joc.8b03218

Showing NP-Card for cladophorol A (NP0333033)

MOL for NP0333033 (cladophorol A)

3D MOL for NP0333033 (cladophorol A)

3D SDF for NP0333033 (cladophorol A)

3D-SDF for NP0333033 (cladophorol A)

PDB for NP0333033 (cladophorol A)

3D PDB for NP0333033 (cladophorol A)

SMILES for NP0333033 (cladophorol A)

INCHI for NP0333033 (cladophorol A)

Structure for NP0333033 (cladophorol A)

3D Structure for NP0333033 (cladophorol A)