PDBe-KB Ligand Pages (PDBeChem)

Examples: STI GLC NAG HEM CLC_000191 PRD_000468

DQH

(2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE

Description

Synonyms

(+)-taxifolin, Dihydroquercetin, (+)-dihydroquercetin, (2R,3...Show more

Formula

C15 H12 O7

IUPAC InChI

InChI=1S/C15H12O7/c16-7-4-10(19)12-11(5-7)22-15(14(21)13(12)20)6-1-2-8(17)9(18)3-6/h1-5,14-19,21H/t14-,15+/m0/s1

IUPAC InChIKey

CXQWRCVTCMQVQX-LSDHHAIUSA-N

SMILES

c1cc(c(cc1[C@@H]2[C@H](C(=O)c3c(cc(cc3O2)O)O)O)O)O

Source OpenEye

First observed in

1gp5

Overall view, and highlighted
scaffolds and fragments
This image gallery displays several views of the ligand structure:
Basic Structural Representation: Shows the overall structure of the ligand.
Detailed Structural Representation: Highlights individual atoms within the ligand.
Murcko Scaffold: Presents the scaffold of the ligand highlighted in yellow.
Highlighted Fragments: Displays various ligand fragments, highlighted in yellow.

Displayed: 1 / 2

Physicochemical properties

Molecular properties

Molecular weight

Total mass of the molecule in Daltons

304.1 Da

Labute accessible surface area

Accessible surface area according to the Labute's definition

141.1 Å ²

Heavy atoms

Number of non-hydrogen atoms

Heteroatoms

Number of non-oxygen and non-carbon atoms

Carbon SP3 value

Fraction of C atoms that are SP3 hybridized

0.1

Wildman-Crippen molar refractivity

Wildman-Crippen molar refractivity is a common descriptor accounting for molecular size and polarizability

69.7

Wildman-Crippen Log P

Octanol/Water partition coefficient predicted using Wildman-Crippen method

-1.2

Conformational properties

Rotatable bonds

Number of single bonds, not part of a ring bound to a nonterminal heavy atom

Ring properties

Aromatic rings

Number of aromatic rings

Rings

Number of rings

Aliphatic rings

Number of aliphatic rings

Heterocycles

Number or rings with at least two different elements

Saturated rings

Number of saturated rings

Aromatic heterocycles

Number of aromatic heterocyles

Saturated heterocycles

Number of saturated heterocyles

Aliphatic heterocycles

Number of aliphatic heterocycles

Spiro atoms

Atoms shared between rings that share exactly one atom

Bridgehead atoms

Number of atoms shared between rings that share at least two bonds

Surface properties

Topological surface area

127.5

Functional group properties

Hydrogen bond donors

Number of hydrogen bond donors

Hydrogen bond acceptors

Number of hydrogen bond acceptors

Amide bonds

Number of amide bonds

Stereochemical properties

Stereocenters

Number of atoms with four attachments different from each other

Bound structures

Found as a bound ligand in 6 distinct proteins and 7 PDB Structures. Group data by:

Proteins

Structures

Protein name

Protein Overview

Total structures

Organism

EC number

Ligand function

Chalcone isomerase N-terminal domain-containing protein

V9P0A9

Eubacterium ramulus

5.5.1.6

Unannotated

Flavanone 4-reductase

P93799

Vitis vinifera (Grape)

1.1.1.234, 1.1.1.219

Unannotated

NAD-dependent epimerase/dehydratase domain-containing protein

C5YGL7

Sorghum bicolor (Sorghum)

Unannotated

Tetracenomycin biosynthesis bifunctional cyclase/O-methyl transferase TcmN

P16559

Streptomyces glaucescens

2.1.1.-, 2.3.1.235

Unannotated

Leucoanthocyanidin dioxygenase

Q96323

Arabidopsis thaliana (Mouse-ear cress)

1.14.20.4

Unannotated

Flavanone 4-reductase

A0A8T0SQV2

Panicum virgatum (Blackwell switchgrass)

1.1.1.234, 1.1.1.219

Unannotated

Page Size:

1 to 6 of 6

Page 1 of 1

Protein name

Chalcone isomerase N-terminal domain-containing protein

PDB-KB Proteins

V9P0A9

EC number

5.5.1.6

Ligand annotation

Unannotated

Total structures

Protein name

Flavanone 4-reductase

PDB-KB Proteins

P93799

EC number

1.1.1.234, 1.1.1.219

Ligand annotation

Unannotated

Total structures

Protein name

NAD-dependent epimerase/dehydratase domain-containing protein

PDB-KB Proteins

C5YGL7

EC number

---

Ligand annotation

Unannotated

Total structures

Protein name

Tetracenomycin biosynthesis bifunctional cyclase/O-methyl transferase TcmN

PDB-KB Proteins

P16559

EC number

2.1.1.-, 2.3.1.235

Ligand annotation

Unannotated

Total structures

Protein name

Leucoanthocyanidin dioxygenase

PDB-KB Proteins

Q96323

EC number

1.14.20.4

Ligand annotation

Unannotated

Total structures

Items per page:

1 – 5 of 6

Interaction statistics

Interaction statistics shows the summary of aggregated protein-ligand interaction data of DQH from 63 ligand instances in 6 PDB structures and 7 PDB chains. The protein-ligand interactions are computed using PDBe Arpeggio

Documentation

Ligand atoms

Sort by:

Amino acid properties

Interactions

Ligand interactions

Percentage of interactions by ligand atom compared to the total interactions of the ligand

Amino acid interactions

Percentage of interactions between ligand atom-amino acid pair compared to the total interactions of the amino acid

Icons:

Positively charged

Negatively charged

Polar

Hydrophobic

Aromatic

Aromatic (Trp)

Glycine

Cysteine

Proline

Atom-wise interactions of DQH molecule
Percentage of interactions by ligand atom compared to the total interactions of the ligand

For full interaction statistics, including the heatmap showing ligand atom interaction frequency with different amino acids, please view on a larger screen