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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3zv5

2.400 Å

X-ray

2011-07-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase
ID:BPHB_COMTE
AC:Q46381
Organism:Comamonas testosteroni
Reign:Bacteria
TaxID:285
EC Number:1.3.1.56


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:39.328
Number of residues:26
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: NAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.783411.750

% Hydrophobic% Polar
59.0240.98
According to VolSite

Ligand :
3zv5_1 Structure
HET Code: BPY
Formula: C12H10O2
Molecular weight: 186.207 g/mol
DrugBank ID: DB02923
Buried Surface Area:68.51 %
Polar Surface area: 40.46 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-2.19321-20.988-3.96557


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
CK1CZ2TRP- 903.170Hydrophobic
CK4CBSER- 1424.430Hydrophobic
OK2ND2ASN- 1432.71124.93H-Bond
(Protein Donor)
OK1OHTYR- 1553.07134.96H-Bond
(Ligand Donor)
CK6CD2LEU- 1913.910Hydrophobic
CK6CD1ILE- 2043.520Hydrophobic
CK9CD1LEU- 2093.850Hydrophobic
CKACEMET- 2123.860Hydrophobic
CKBCEMET- 2553.970Hydrophobic