scPDB - 2opq entry

Protein Data Bank Entry:

PDB ID : 2opq

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2007-01-30

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_HV1H2
AC:	P04585
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11706
EC Number:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
B	4 %

Ligand binding site composition:

B-Factor:	52.885
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.497	378.000

% Hydrophobic	% Polar
75.00	25.00
According to VolSite

Ligand :

HET Code:	HBQ
Formula:	C14H17FN2O3
Molecular weight:	280.295 g/mol
DrugBank ID:	DB07884
Buried Surface Area:	78.19 %
Polar Surface area:	58.64 Å2

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

Mass center Coordinates

X	Y	Z
1.79825	-36.8677	20.5224

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
C14	CG	PRO- 95	3.76	0	Hydrophobic	false
C14	CG2	ILE- 100	4.44	0	Hydrophobic	false
C5	CD1	ILE- 100	3.74	0	Hydrophobic	false
N2	O	LYS- 101	2.69	153.11	H-Bond (Ligand Donor)	false
O1	N	LYS- 101	3.14	158.06	H-Bond (Protein Donor)	false
C9	CG	LYS- 103	4.22	0	Hydrophobic	false
C6	CG2	VAL- 106	3.72	0	Hydrophobic	false
C7	CG1	VAL- 106	3.7	0	Hydrophobic	false
C9	CG1	VAL- 179	3.59	0	Hydrophobic	false
C14	CE1	TYR- 181	4.45	0	Hydrophobic	false
C12	CD1	TYR- 181	3.49	0	Hydrophobic	false
C10	CB	TYR- 188	4.27	0	Hydrophobic	false
C13	CD2	TYR- 188	3.5	0	Hydrophobic	false
F1	CD2	PHE- 227	3.43	0	Hydrophobic	false
C13	CE2	TRP- 229	4.18	0	Hydrophobic	false
C14	CZ3	TRP- 229	3.71	0	Hydrophobic	false
F1	CB	LEU- 234	3.45	0	Hydrophobic	false