scPDB - 3qro entry

Protein Data Bank Entry:

PDB ID : 3qro

Resolution :1.620 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	51 %
B	49 %

Ligand binding site composition:

B-Factor:	11.858
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.822	752.625

% Hydrophobic	% Polar
41.26	58.74
According to VolSite

Ligand :

HET Code:	NK9
Formula:	C26H28F3N4O5S
Molecular weight:	565.585 g/mol
DrugBank ID:	-
Buried Surface Area:	71.73 %
Polar Surface area:	157.94 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-17.9366	19.508	-4.76179

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
F35	CD	ARG- 8	4.22	0	Hydrophobic	false
C39	CD2	LEU- 23	3.57	0	Hydrophobic	false
N2	OD1	ASP- 25	2.97	0	Ionic (Ligand Cationic)	false
N2	OD2	ASP- 25	2.79	0	Ionic (Ligand Cationic)	false
N2	OD1	ASP- 25	2.74	0	Ionic (Ligand Cationic)	false
N2	OD2	ASP- 25	3.09	0	Ionic (Ligand Cationic)	false
N5	OD2	ASP- 25	3.44	0	Ionic (Ligand Cationic)	false
N2	OD2	ASP- 25	2.79	156.67	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 25	2.74	171.33	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 25	3.09	124.26	H-Bond (Ligand Donor)	false
N5	OD2	ASP- 25	3.44	120.15	H-Bond (Ligand Donor)	false
C14	CB	ALA- 28	3.72	0	Hydrophobic	false
C23	CB	ALA- 28	3.79	0	Hydrophobic	false
C12	CB	ASP- 30	4.42	0	Hydrophobic	false
O13	N	ASP- 30	2.95	139.05	H-Bond (Protein Donor)	false
O26	N	ASP- 30	2.93	156.21	H-Bond (Protein Donor)	false
O13	OD2	ASP- 30	2.6	158.62	H-Bond (Ligand Donor)	false
C22	CG2	VAL- 32	4.25	0	Hydrophobic	false
C14	CG2	VAL- 32	4.17	0	Hydrophobic	false
C9	CB	ILE- 47	3.9	0	Hydrophobic	false
C12	CD1	ILE- 47	4.27	0	Hydrophobic	false
O10	N	GLY- 48	3.24	127.64	H-Bond (Protein Donor)	false
O10	O	GLY- 48	2.67	169.45	H-Bond (Ligand Donor)	false
C8	CG2	ILE- 50	4.48	0	Hydrophobic	false
C21	CD1	ILE- 50	3.5	0	Hydrophobic	false
O18	N	ILE- 50	2.96	154.65	H-Bond (Protein Donor)	false
O19	N	ILE- 50	2.92	166.3	H-Bond (Protein Donor)	false
F37	CB	PRO- 81	3.59	0	Hydrophobic	false
C32	CG	PRO- 81	3.63	0	Hydrophobic	false
F37	CG1	VAL- 82	4.3	0	Hydrophobic	false
C38	CG2	VAL- 82	3.87	0	Hydrophobic	false
C14	CD1	ILE- 84	3.79	0	Hydrophobic	false
C21	CD1	ILE- 84	3.64	0	Hydrophobic	false
C29	CD1	ILE- 84	3.56	0	Hydrophobic	false