scPDB - 3koo entry

Protein Data Bank Entry:

PDB ID : 3koo

Resolution :2.790 Å

Experimental Method : X-ray

Deposition Date : 2009-11-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Bifunctional epoxide hydrolase 2
ID:	HYES_HUMAN
AC:	P34913
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.3.2.10

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	69.975
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.619	745.875

% Hydrophobic	% Polar
64.25	35.75
According to VolSite

Ligand :

HET Code:	24D
Formula:	C17H18Cl2N4O2
Molecular weight:	381.256 g/mol
DrugBank ID:	-
Buried Surface Area:	67.73 %
Polar Surface area:	67.35 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
75.3575	-7.05076	64.5717

Binding mode :

What is Poseview ?

2D View
3D View

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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
CL24	CD1	PHE- 267	3.53	0	Hydrophobic	false
N7	OD1	ASP- 335	3	124.5	H-Bond (Ligand Donor)	false
C12	CZ2	TRP- 336	3.82	0	Hydrophobic	false
C13	CE2	TRP- 336	4.19	0	Hydrophobic	false
C13	CE	MET- 339	4.28	0	Hydrophobic	false
C14	CG2	THR- 360	4.26	0	Hydrophobic	false
C20	CG	PRO- 361	4.02	0	Hydrophobic	false
C20	CG1	ILE- 363	4.45	0	Hydrophobic	false
O9	OH	TYR- 383	2.86	167.2	H-Bond (Protein Donor)	false
C25	SD	MET- 419	4.46	0	Hydrophobic	false
CL1	CE	MET- 419	3.85	0	Hydrophobic	false
O9	OH	TYR- 466	3.13	149.01	H-Bond (Protein Donor)	false
CL1	CE1	PHE- 497	3.57	0	Hydrophobic	false
C3	CB	VAL- 498	3.55	0	Hydrophobic	false
C4	CG1	VAL- 498	3.95	0	Hydrophobic	false
C2	CG2	VAL- 498	4.13	0	Hydrophobic	false
C14	CD2	LEU- 499	3.74	0	Hydrophobic	false
C20	CD2	LEU- 499	3.95	0	Hydrophobic	false
C20	SD	MET- 503	4.12	0	Hydrophobic	false
DuAr	DuAr	HIS- 524	3.64	0	Aromatic Face/Face	false
CL1	CB	HIS- 524	3.67	0	Hydrophobic	false
CL24	CH2	TRP- 525	4.38	0	Hydrophobic	false