scPDB - 3rga entry

Protein Data Bank Entry:

PDB ID : 3rga

Resolution :1.590 Å

Experimental Method : X-ray

Deposition Date : 2011-04-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Epoxide hydrolase LasB
ID:	LSD19_STRLS
AC:	B6ZK72
Organism:	Streptomyces lasaliensis
Reign:	Bacteria
TaxID:	324833
EC Number:	5.5.1

Chains:

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

Ligand binding site composition:

B-Factor:	19.090
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.018	540.000

% Hydrophobic	% Polar
53.13	46.88
According to VolSite

Ligand :

HET Code:	LSB
Formula:	C29H43NO6
Molecular weight:	501.655 g/mol
DrugBank ID:	-
Buried Surface Area:	65.41 %
Polar Surface area:	91.9 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	4
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
53.2103	51.2057	12.5692

Binding mode :

What is Poseview ?

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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
O33	OH	TYR- 14	2.78	169.56	H-Bond (Protein Donor)	false
C20	CE2	TYR- 14	4.16	0	Hydrophobic	false
C23	CE2	TYR- 14	4.17	0	Hydrophobic	false
C35	SG	CYS- 15	3.3	0	Hydrophobic	false
C32	CD2	LEU- 36	4.19	0	Hydrophobic	false
O29	OD2	ASP- 38	2.75	152.54	H-Bond (Ligand Donor)	false
C32	CD2	LEU- 55	3.63	0	Hydrophobic	false
C30	CB	ALA- 58	3.83	0	Hydrophobic	false
C30	CG2	VAL- 63	4.21	0	Hydrophobic	false
O33	OE2	GLU- 65	2.6	154.64	H-Bond (Protein Donor)	false
C35	CD2	LEU- 81	3.54	0	Hydrophobic	false
C35	CB	ALA- 83	3.78	0	Hydrophobic	false
C15	CG1	VAL- 85	4.02	0	Hydrophobic	false
C17	CG1	VAL- 85	4.46	0	Hydrophobic	false
C19	CG2	VAL- 85	4.38	0	Hydrophobic	false
C21	CG2	VAL- 85	4.45	0	Hydrophobic	false
C30	CG1	VAL- 85	4.37	0	Hydrophobic	false
C28	CG2	THR- 100	3.28	0	Hydrophobic	false
C34	CG2	VAL- 102	4	0	Hydrophobic	false
C21	CG2	VAL- 102	4.11	0	Hydrophobic	false
C28	CG1	VAL- 102	3.57	0	Hydrophobic	false
C23	CD1	ILE- 106	4.31	0	Hydrophobic	false
C24	CG1	ILE- 106	4.06	0	Hydrophobic	false
C23	SD	MET- 117	3.75	0	Hydrophobic	false
C24	CE	MET- 117	3.9	0	Hydrophobic	false
C20	CG2	VAL- 119	3.99	0	Hydrophobic	false
C21	CG1	VAL- 119	4.4	0	Hydrophobic	false
C23	CG2	VAL- 119	4.24	0	Hydrophobic	false
C28	CE2	TRP- 121	3.6	0	Hydrophobic	false