scPDB - 3i6o entry

Protein Data Bank Entry:

PDB ID : 3i6o

Resolution :1.170 Å

Experimental Method : X-ray

Deposition Date : 2009-07-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Gag-Pol polyprotein
ID:	POL_HV1BR
AC:	P03367
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11686
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	52 %
B	48 %

Ligand binding site composition:

B-Factor:	13.559
Number of residues:	47
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	IOD IOD

Cavity properties

Ligandability	Volume (Å3)
0.798	732.375

% Hydrophobic	% Polar
42.40	57.60
According to VolSite

Ligand :

HET Code:	GR6
Formula:	C32H42N2O9S
Molecular weight:	630.749 g/mol
DrugBank ID:	-
Buried Surface Area:	71.2 %
Polar Surface area:	141.24 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
17.0096	-20.3837	-5.27068

Binding mode :

What is Poseview ?

2D View
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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
O17	OD1	ASP- 25	2.82	157.26	H-Bond (Protein Donor)	false
N19	O	GLY- 27	3.03	165.27	H-Bond (Ligand Donor)	false
C24	CB	ALA- 28	3.84	0	Hydrophobic	false
C26	CB	ASP- 29	3.94	0	Hydrophobic	false
O27	N	ASP- 29	2.95	163.11	H-Bond (Protein Donor)	false
C24	CB	ASP- 30	4.23	0	Hydrophobic	false
C26	CB	ASP- 30	4.44	0	Hydrophobic	false
O25	N	ASP- 30	3.23	159.53	H-Bond (Protein Donor)	false
C24	CG2	VAL- 32	4.06	0	Hydrophobic	false
C24	CD1	ILE- 47	4.4	0	Hydrophobic	false
C5	CD1	ILE- 50	4.21	0	Hydrophobic	false
C36	CB	ILE- 50	4.19	0	Hydrophobic	false
C14	CG	PRO- 81	4.39	0	Hydrophobic	false
C14	CB	VAL- 82	3.88	0	Hydrophobic	false
C24	CD1	ILE- 84	4.12	0	Hydrophobic	false
C13	CG2	ILE- 84	3.77	0	Hydrophobic	false
C32	CD2	LEU- 123	3.81	0	Hydrophobic	false
O17	OD2	ASP- 125	2.51	162.26	H-Bond (Ligand Donor)	false
C15	CB	ALA- 128	4.06	0	Hydrophobic	false
C6	CB	ALA- 128	3.55	0	Hydrophobic	false
C5	CB	ALA- 128	3.47	0	Hydrophobic	false
C39	CB	ASP- 129	3.64	0	Hydrophobic	false
O38	N	ASP- 130	3	134.48	H-Bond (Protein Donor)	false
C39	CB	ASP- 130	3.93	0	Hydrophobic	false
C6	CG2	VAL- 132	3.87	0	Hydrophobic	false
C39	CG2	ILE- 147	4.22	0	Hydrophobic	false
C23	CD1	ILE- 150	4.21	0	Hydrophobic	false
C13	CD1	ILE- 150	3.84	0	Hydrophobic	false
C34	CB	PRO- 181	3.85	0	Hydrophobic	false
C35	CG	PRO- 181	3.67	0	Hydrophobic	false
C33	CG2	VAL- 182	3.38	0	Hydrophobic	false
C31	CD1	ILE- 184	3.81	0	Hydrophobic	false