scPDB - 3qbf entry

Protein Data Bank Entry:

PDB ID : 3qbf

Resolution :1.450 Å

Experimental Method : X-ray

Deposition Date : 2011-01-13

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:	12.052
Number of residues:	43
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.788	803.250

% Hydrophobic	% Polar
39.92	60.08
According to VolSite

Ligand :

HET Code:	JHG
Formula:	C28H32F3N4O3S
Molecular weight:	561.639 g/mol
DrugBank ID:	-
Buried Surface Area:	69.15 %
Polar Surface area:	117.48 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
18.2112	-19.7487	-5.06892

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
C27	CD2	LEU- 23	3.96	0	Hydrophobic	false
N3	OD2	ASP- 25	3.27	0	Ionic (Ligand Cationic)	false
N16	OD2	ASP- 25	2.89	0	Ionic (Ligand Cationic)	false
N16	OD1	ASP- 25	2.9	0	Ionic (Ligand Cationic)	false
N16	OD1	ASP- 25	2.75	0	Ionic (Ligand Cationic)	false
N16	OD2	ASP- 25	2.97	0	Ionic (Ligand Cationic)	false
N16	OD2	ASP- 25	2.89	144.6	H-Bond (Ligand Donor)	false
N16	OD1	ASP- 25	2.75	153.27	H-Bond (Ligand Donor)	false
N16	OD2	ASP- 25	2.97	139.65	H-Bond (Ligand Donor)	false
C6	CB	ALA- 28	3.5	0	Hydrophobic	false
C33	CB	ALA- 28	3.93	0	Hydrophobic	false
F10	CB	ASP- 29	3.37	0	Hydrophobic	false
N36	OD1	ASP- 30	3.17	158	H-Bond (Ligand Donor)	false
O37	N	ASP- 30	3.05	148.81	H-Bond (Protein Donor)	false
F10	CB	ASP- 30	3.37	0	Hydrophobic	false
F11	CG2	VAL- 32	4.08	0	Hydrophobic	false
C33	CG2	VAL- 32	4.21	0	Hydrophobic	false
C7	CG2	VAL- 32	3.66	0	Hydrophobic	false
F12	CB	ILE- 47	3.57	0	Hydrophobic	false
C13	CB	ILE- 47	4.31	0	Hydrophobic	false
C8	CD1	ILE- 47	4.22	0	Hydrophobic	false
F11	CG2	ILE- 47	3.25	0	Hydrophobic	false
C5	CB	ILE- 50	4.21	0	Hydrophobic	false
C14	CG2	ILE- 50	4.03	0	Hydrophobic	false
C32	CD1	ILE- 50	3.37	0	Hydrophobic	false
O29	N	ILE- 50	2.93	169.25	H-Bond (Protein Donor)	false
O30	N	ILE- 50	3.08	157.06	H-Bond (Protein Donor)	false
F11	CD1	LEU- 76	3.7	0	Hydrophobic	false
C20	CG	PRO- 81	4.35	0	Hydrophobic	false
C23	CG	PRO- 81	3.51	0	Hydrophobic	false
C24	CB	PRO- 81	3.59	0	Hydrophobic	false
C27	CG2	VAL- 82	3.79	0	Hydrophobic	false
C26	CG1	VAL- 82	3.9	0	Hydrophobic	false
C6	CG2	ILE- 84	4.32	0	Hydrophobic	false
C19	CD1	ILE- 84	4.15	0	Hydrophobic	false
C21	CD1	ILE- 84	4.42	0	Hydrophobic	false