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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:

5alu

1.870 Å

X-ray

2015-03-08

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:19.281
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.189405.000

% Hydrophobic% Polar
54.1745.83
According to VolSite

Ligand :
5alu_2 Structure
HET Code: HD2
Formula: C24H34N4O3
Molecular weight: 426.552 g/mol
DrugBank ID: -
Buried Surface Area:69.04 %
Polar Surface area: 96.37 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 3
Rings: 7
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-15.4867-10.59514.8369


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
C21CG2ILE- 3633.780Hydrophobic
C19CBSER- 3743.80Hydrophobic
C24CG1ILE- 3753.770Hydrophobic
C25CGPHE- 3813.80Hydrophobic
C17CD2PHE- 3813.690Hydrophobic
O26OE1GLN- 3842.71163.65H-Bond
(Ligand Donor)
C24SDMET- 4694.380Hydrophobic
C8CEMET- 5034.360Hydrophobic
C9CGMET- 5034.030Hydrophobic