scPDB - 3opd entry

Protein Data Bank Entry:

PDB ID : 3opd

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2010-08-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Heat shock protein 83
ID:	HSP83_TRYBB
AC:	P12861
Organism:	Trypanosoma brucei brucei
Reign:	Eukaryota
TaxID:	5702
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	98 %
B	2 %

Ligand binding site composition:

B-Factor:	43.065
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.346	1053.000

% Hydrophobic	% Polar
50.64	49.36
According to VolSite

Ligand :

HET Code:	HIE
Formula:	C23H27F3N4O3
Molecular weight:	464.481 g/mol
DrugBank ID:	-
Buried Surface Area:	70.7 %
Polar Surface area:	110.24 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-1.48648	16.4779	12.2757

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
C1	CB	ASN- 36	3.71	0	Hydrophobic	false
C12	CD	LYS- 43	3.58	0	Hydrophobic	false
N1	OD2	ASP- 78	2.9	172.68	H-Bond (Ligand Donor)	false
C12	CG2	ILE- 81	4.31	0	Hydrophobic	false
C9	CG2	ILE- 81	4.42	0	Hydrophobic	false
C8	SD	MET- 83	4.16	0	Hydrophobic	false
C17	SD	MET- 83	4.26	0	Hydrophobic	false
C22	SD	MET- 83	4	0	Hydrophobic	false
C5	CE	MET- 83	3.59	0	Hydrophobic	false
C1	CE	MET- 83	4.22	0	Hydrophobic	false
C4	SD	MET- 83	3.77	0	Hydrophobic	false
C9	CG	MET- 83	3.27	0	Hydrophobic	false
C21	CD2	LEU- 88	3.92	0	Hydrophobic	false
C22	CD2	LEU- 88	4.01	0	Hydrophobic	false
C19	CB	ASN- 91	4.42	0	Hydrophobic	false
C8	CD1	LEU- 92	4.29	0	Hydrophobic	false
F1	CB	LEU- 92	3.53	0	Hydrophobic	false
C22	CG	LEU- 92	4.03	0	Hydrophobic	false
C4	CD1	LEU- 92	3.72	0	Hydrophobic	false
C10	CD2	LEU- 92	3.69	0	Hydrophobic	false
C23	CD1	LEU- 92	4.07	0	Hydrophobic	false
F3	CD1	ILE- 95	3.41	0	Hydrophobic	false
F1	CB	ALA- 96	3.31	0	Hydrophobic	false
F2	CG1	VAL- 121	3.81	0	Hydrophobic	false
F3	CG1	VAL- 121	4.3	0	Hydrophobic	false
C21	CZ	PHE- 123	4.22	0	Hydrophobic	false
C17	CG	PHE- 123	4.02	0	Hydrophobic	false
C2	CB	PHE- 123	3.79	0	Hydrophobic	false
C19	CE2	PHE- 123	3.8	0	Hydrophobic	false
C19	CZ	TYR- 124	4.33	0	Hydrophobic	false
F2	CE1	TYR- 124	3.29	0	Hydrophobic	false
O1	OH	TYR- 124	2.8	128.44	H-Bond (Protein Donor)	false
C21	CG2	VAL- 135	4.2	0	Hydrophobic	false
C19	CZ2	TRP- 147	4.17	0	Hydrophobic	false
C21	CD2	TRP- 147	3.34	0	Hydrophobic	false
C18	CE2	TRP- 147	4.46	0	Hydrophobic	false
C1	CD1	ILE- 171	3.6	0	Hydrophobic	false
N4	O	HOH- 248	2.95	160.88	H-Bond (Protein Donor)	false
O2	O	HOH- 355	2.95	179.98	H-Bond (Protein Donor)	false