scPDB - 2pqz entry

Protein Data Bank Entry:

PDB ID : 2pqz

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2007-05-03

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	53 %
B	47 %

Ligand binding site composition:

B-Factor:	13.960
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.810	803.250

% Hydrophobic	% Polar
42.02	57.98
According to VolSite

Ligand :

HET Code:	G0G
Formula:	C30H32N3O4S2
Molecular weight:	562.723 g/mol
DrugBank ID:	-
Buried Surface Area:	71.18 %
Polar Surface area:	108.13 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
11.5722	-19.9884	-17.6195

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	CD2	LEU- 23	3.81	0	Hydrophobic	false
C39	CD2	LEU- 23	4.12	0	Hydrophobic	false
N22	OD2	ASP- 25	2.87	130.88	H-Bond (Ligand Donor)	false
N22	OD1	ASP- 25	2.99	163.2	H-Bond (Ligand Donor)	false
N22	OD2	ASP- 25	2.6	135.98	H-Bond (Ligand Donor)	false
N22	OD2	ASP- 25	2.87	0	Ionic (Ligand Cationic)	false
N22	OD1	ASP- 25	2.99	0	Ionic (Ligand Cationic)	false
N22	OD1	ASP- 25	3.02	0	Ionic (Ligand Cationic)	false
N22	OD2	ASP- 25	2.6	0	Ionic (Ligand Cationic)	false
C20	CB	ALA- 28	3.77	0	Hydrophobic	false
C4	CB	ALA- 28	3.79	0	Hydrophobic	false
C6	CB	ASP- 30	4.05	0	Hydrophobic	false
C5	CG2	VAL- 32	3.61	0	Hydrophobic	false
C1	CG2	VAL- 32	3.65	0	Hydrophobic	false
C2	CB	ILE- 47	4.07	0	Hydrophobic	false
C6	CG2	ILE- 47	4.26	0	Hydrophobic	false
C4	CD1	ILE- 47	4.43	0	Hydrophobic	false
C5	CD1	ILE- 47	4.33	0	Hydrophobic	false
O10	N	ILE- 50	3.34	154.08	H-Bond (Protein Donor)	false
O41	N	ILE- 50	2.88	167.8	H-Bond (Protein Donor)	false
C35	CB	ILE- 50	4.34	0	Hydrophobic	false
C1	CD1	ILE- 50	3.62	0	Hydrophobic	false
C17	CD1	ILE- 50	3.29	0	Hydrophobic	false
C13	CG	PRO- 81	3.53	0	Hydrophobic	false
C13	CG	PRO- 81	3.53	0	Hydrophobic	false
C14	CG1	VAL- 82	4.13	0	Hydrophobic	false
C39	CG1	VAL- 82	3.98	0	Hydrophobic	false
C1	CG2	ILE- 84	4.24	0	Hydrophobic	false
C17	CG1	ILE- 84	4.29	0	Hydrophobic	false
C14	CD1	ILE- 84	3.87	0	Hydrophobic	false
C33	CD1	ILE- 84	3.72	0	Hydrophobic	false
C38	CD1	ILE- 84	3.65	0	Hydrophobic	false