scPDB - 3qrs entry

Protein Data Bank Entry:

PDB ID : 3qrs

Resolution :1.590 Å

Experimental Method : X-ray

Deposition Date : 2011-02-18

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	48 %
B	52 %

Ligand binding site composition:

B-Factor:	10.796
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.880	772.875

% Hydrophobic	% Polar
45.41	54.59
According to VolSite

Ligand :

HET Code:	NK8
Formula:	C27H29F3N5O4S
Molecular weight:	576.610 g/mol
DrugBank ID:	-
Buried Surface Area:	70.4 %
Polar Surface area:	160.57 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-18.3674	19.6433	-4.84183

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	CD2	LEU- 23	3.78	0	Hydrophobic	false
N27	OD2	ASP- 25	3.33	0	Ionic (Ligand Cationic)	false
N40	OD2	ASP- 25	2.89	0	Ionic (Ligand Cationic)	false
N40	OD1	ASP- 25	2.98	0	Ionic (Ligand Cationic)	false
N40	OD1	ASP- 25	2.75	0	Ionic (Ligand Cationic)	false
N40	OD2	ASP- 25	3.04	0	Ionic (Ligand Cationic)	false
N40	OD2	ASP- 25	2.89	150.31	H-Bond (Ligand Donor)	false
N40	OD1	ASP- 25	2.75	167.48	H-Bond (Ligand Donor)	false
N40	OD2	ASP- 25	3.04	128.94	H-Bond (Ligand Donor)	false
C30	CB	ALA- 28	3.52	0	Hydrophobic	false
C21	CB	ALA- 28	3.72	0	Hydrophobic	false
O19	N	ASP- 30	3.09	143.72	H-Bond (Protein Donor)	false
O35	N	ASP- 30	3.12	147.83	H-Bond (Protein Donor)	false
N20	OD1	ASP- 30	3	163.71	H-Bond (Ligand Donor)	false
C21	CG2	VAL- 32	4.13	0	Hydrophobic	false
C30	CG2	VAL- 32	3.82	0	Hydrophobic	false
C31	CD1	ILE- 47	4.25	0	Hydrophobic	false
C32	CB	ILE- 47	4.27	0	Hydrophobic	false
O23	N	ILE- 50	2.96	170.27	H-Bond (Protein Donor)	false
O24	N	ILE- 50	3	159.62	H-Bond (Protein Donor)	false
C29	CD1	ILE- 50	4.45	0	Hydrophobic	false
C37	CG2	ILE- 50	4.41	0	Hydrophobic	false
C22	CD1	ILE- 50	3.33	0	Hydrophobic	false
C21	CD1	ILE- 50	3.58	0	Hydrophobic	false
F7	CB	PRO- 81	3.6	0	Hydrophobic	false
C8	CG	PRO- 81	3.69	0	Hydrophobic	false
F5	CG1	VAL- 82	4.03	0	Hydrophobic	false
C2	CG2	VAL- 82	3.98	0	Hydrophobic	false
C30	CD1	ILE- 84	4.28	0	Hydrophobic	false
C11	CD1	ILE- 84	3.74	0	Hydrophobic	false
C22	CD1	ILE- 84	3.54	0	Hydrophobic	false