scPDB - 3bgb entry

Protein Data Bank Entry:

PDB ID : 3bgb

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-11-26

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_HV1B5
AC:	P04587
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11682
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	50 %
B	50 %

Ligand binding site composition:

B-Factor:	25.949
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.979	843.750

% Hydrophobic	% Polar
41.20	58.80
According to VolSite

Ligand :

HET Code:	LJG
Formula:	C24H40N5O4S2
Molecular weight:	526.735 g/mol
DrugBank ID:	-
Buried Surface Area:	72.52 %
Polar Surface area:	160.16 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
12.0607	-20.2334	-17.4849

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
C25	CD2	LEU- 23	4.29	0	Hydrophobic	false
C10	CD2	LEU- 23	3.42	0	Hydrophobic	false
N1	OD2	ASP- 25	3.22	0	Ionic (Ligand Cationic)	false
N1	OD1	ASP- 25	3.75	0	Ionic (Ligand Cationic)	false
N1	OD1	ASP- 25	3.56	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 25	2.82	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 25	2.82	158.02	H-Bond (Ligand Donor)	false
C6	CB	ALA- 28	4.27	0	Hydrophobic	false
C3	CB	ALA- 28	4.48	0	Hydrophobic	false
C31	CB	ALA- 28	3.44	0	Hydrophobic	false
C17	CB	ALA- 28	3.7	0	Hydrophobic	false
N33	O	ASP- 30	3.01	142.1	H-Bond (Ligand Donor)	false
N19	O	ASP- 30	3.13	143.28	H-Bond (Ligand Donor)	false
C31	CG2	VAL- 32	3.49	0	Hydrophobic	false
C17	CG1	VAL- 32	3.76	0	Hydrophobic	false
C15	CB	ILE- 47	3.91	0	Hydrophobic	false
C30	CD1	ILE- 47	4.07	0	Hydrophobic	false
C29	CB	ILE- 47	3.93	0	Hydrophobic	false
C16	CD1	ILE- 47	3.91	0	Hydrophobic	false
C24	CD1	ILE- 50	4.02	0	Hydrophobic	false
C18	CD1	ILE- 50	4.17	0	Hydrophobic	false
C32	CD1	ILE- 50	3.8	0	Hydrophobic	false
O35	N	ILE- 50	3.47	127.07	H-Bond (Protein Donor)	false
C24	CG	PRO- 81	3.55	0	Hydrophobic	false
C11	CG	PRO- 81	3.67	0	Hydrophobic	false
C10	CG1	VAL- 82	4.27	0	Hydrophobic	false
C11	CG1	VAL- 82	3.91	0	Hydrophobic	false
C25	CG1	VAL- 82	3.3	0	Hydrophobic	false
C32	CD1	ILE- 84	4.05	0	Hydrophobic	false
C31	CG2	ILE- 84	4.37	0	Hydrophobic	false
C18	CD1	ILE- 84	4.13	0	Hydrophobic	false
C25	CD1	ILE- 84	3.3	0	Hydrophobic	false
C11	CD1	ILE- 84	3.45	0	Hydrophobic	false