NP-MRD: Showing NP-Card for 5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol (NP0189424)

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Record Information

Version

2.0

Created at

2022-09-04 05:54:10 UTC

Updated at

2022-09-04 05:54:10 UTC

NP-MRD ID

NP0189424

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol

Description

SCHEMBL172418 belongs to the class of organic compounds known as 7-hydroxyflavonoids. These are flavonoids that bear one hydroxyl group at the C-7 position of the flavonoid skeleton. 5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol is found in Pithecellobium clypearia. Based on a literature review very few articles have been published on SCHEMBL172418.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 37  0  0  0  0  0  0  0  0999 V2000
   -5.2996    1.2676    1.8636 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3077    0.7569    1.0274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5948    0.1239   -0.1568 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6206   -0.3952   -1.0103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9863   -1.0213   -2.1917 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3065   -0.2602   -0.6350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9593    0.3771    0.5629 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9714    0.8634    1.3521 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6193    0.4771    0.8752 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2226   -0.6430    0.6496 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6303   -0.2559    0.4688 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9400    0.8089   -0.3348 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2652    1.1779   -0.5107 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5950    2.2566   -1.3235 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2688    0.4790    0.1184 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6147    0.8066   -0.0235 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9366   -0.6051    0.9351 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9066   -1.3454    1.5937 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6123   -0.9669    1.1056 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1951   -1.4637   -0.5207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1763   -0.7546   -1.4298 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5795    2.2448    1.6922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6356    0.0175   -0.4526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2807   -1.3839   -2.7958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6938    1.3651    2.2898 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1610   -1.2657    1.5737 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1839    1.3932   -0.8537 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8903    2.7904   -1.7987 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8327    1.5936   -0.6185 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8917   -1.1170    1.4987 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3761   -1.8242    1.7536 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7100   -2.3947   -0.1764 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6564   -1.7891   -1.1539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4157   -1.4626   -2.2285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6321    0.1489   -1.8159 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  4  6  2  0
  6 21  1  0
 21 20  1  0
 20 10  1  0
 10  9  1  0
  9  7  1  0
  7  8  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
  8  2  1  0
 19 11  1  0
  7  6  1  0
  1 22  1  0
  3 23  1  0
  5 24  1  0
 21 34  1  0
 21 35  1  0
 20 32  1  0
 20 33  1  0
 10 26  1  1
  8 25  1  0
 12 27  1  0
 14 28  1  0
 16 29  1  0
 18 30  1  0
 19 31  1  0
M  END


  Mrv1652309042207542D          

 21 23  0  0  1  0            999 V2000
   -1.4289    0.0000    0.0000 O   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
   -0.7145   -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
    0.0000   -2.4750    0.0000 O   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  2  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
    3.5724    2.0625    0.0000 O   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 O   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
    5.0013   -0.4125    0.0000 O   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
    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  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 11 19  1  0  0  0  0
 10 20  1  0  0  0  0
 20 21  1  0  0  0  0
  6 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0189424

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC(O)=C2CC[C@H](OC2=C1)C1=CC(O)=C(O)C(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H14O6/c16-8-5-10(17)9-1-2-13(21-14(9)6-8)7-3-11(18)15(20)12(19)4-7/h3-6,13,16-20H,1-2H2/t13-/m0/s1

> <INCHI_KEY>
VBMMNHVFWRTWNL-ZDUSSCGKSA-N

> <FORMULA>
C15H14O6

> <MOLECULAR_WEIGHT>
290.271

> <EXACT_MASS>
290.079038171

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
28.278439966013032

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-[(2S)-5,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-2-yl]benzene-1,2,3-triol

> <JCHEM_LOGP>
2.5664453006666665

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.612581991335396

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.754152937779855

> <JCHEM_PKA_STRONGEST_BASIC>
-4.899757116314524

> <JCHEM_POLAR_SURFACE_AREA>
110.38000000000001

> <JCHEM_REFRACTIVITY>
74.6191

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
5-[(2S)-5,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-2-yl]benzene-1,2,3-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.334  -0.770   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       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  -0.000   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       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       8.002  -0.000   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  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   21                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7    2                                                       
CONECT    9    7   10                                                       
CONECT   10    9   11   20                                                  
CONECT   11   10   12   19                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   11                                                       
CONECT   20   10   21                                                       
CONECT   21   20    6                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₁₄O₆

Average Mass

290.2710 Da

Monoisotopic Mass

290.07904 Da

IUPAC Name

5-[(2S)-5,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-2-yl]benzene-1,2,3-triol

Traditional Name

5-[(2S)-5,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-2-yl]benzene-1,2,3-triol

CAS Registry Number

Not Available

SMILES

OC1=CC(O)=C2CC[C@H](OC2=C1)C1=CC(O)=C(O)C(O)=C1

InChI Identifier

InChI=1S/C15H14O6/c16-8-5-10(17)9-1-2-13(21-14(9)6-8)7-3-11(18)15(20)12(19)4-7/h3-6,13,16-20H,1-2H2/t13-/m0/s1

InChI Key

VBMMNHVFWRTWNL-ZDUSSCGKSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Archidendron clypearia	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 7-hydroxyflavonoids. These are flavonoids that bear one hydroxyl group at the C-7 position of the flavonoid skeleton.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Hydroxyflavonoids

Direct Parent

7-hydroxyflavonoids

Alternative Parents

Substituents

3'-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Flavan
1-benzopyran
Benzopyran
Chromane
Pyrogallol derivative
Benzenetriol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Benzenoid
Monocyclic benzene moiety
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
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	2.57	ChemAxon
pKa (Strongest Acidic)	8.75	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	110.38 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	74.62 m³·mol⁻¹	ChemAxon
Polarizability	28.28 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

44236854

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol (NP0189424)

MOL for NP0189424 (5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol)

3D MOL for NP0189424 (5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol)

3D SDF for NP0189424 (5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol)

3D-SDF for NP0189424 (5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol)

PDB for NP0189424 (5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol)

3D PDB for NP0189424 (5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol)

SMILES for NP0189424 (5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol)

INCHI for NP0189424 (5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol)

Structure for NP0189424 (5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol)

3D Structure for NP0189424 (5-[(2s)-5,7-dihydroxy-3,4-dihydro-2h-1-benzopyran-2-yl]benzene-1,2,3-triol)