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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:

5akk

1.900 Å

X-ray

2015-03-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Bifunctional epoxide hydrolase 2
ID:HYES_HUMAN
AC:P34913
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.1.3.76


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:41.034
Number of residues:22
Including
Standard Amino Acids: 19
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.535671.625

% Hydrophobic% Polar
57.7942.21
According to VolSite

Ligand :
5akk_2 Structure
HET Code: 1P8
Formula: C8H6BrNO
Molecular weight: 212.043 g/mol
DrugBank ID: -
Buried Surface Area:47.19 %
Polar Surface area: 29.1 Å2
Number of
H-Bond Acceptors: 1
H-Bond Donors: 1
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
12.0275-8.56127-26.3242


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
C4CBPRO- 3713.370Hydrophobic
BR1CBSER- 3744.130Hydrophobic
C11CD1ILE- 3753.920Hydrophobic
BR1CG1ILE- 3753.460Hydrophobic
C6CBMET- 4694.150Hydrophobic
C11CEMET- 4694.290Hydrophobic
O8ND2ASN- 4722.85155.56H-Bond
(Protein Donor)
C6CBASN- 4723.840Hydrophobic
O8OHOH- 22953.03179.95H-Bond
(Protein Donor)