scPDB - 4gb2 entry

Protein Data Bank Entry:

PDB ID : 4gb2

Resolution :1.790 Å

Experimental Method : X-ray

Deposition Date : 2012-07-26

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_HV1BR
AC:	P03367
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11686
EC Number:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	51 %
B	49 %

Ligand binding site composition:

B-Factor:	18.294
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.608	685.125

% Hydrophobic	% Polar
40.89	59.11
According to VolSite

Ligand :

HET Code:	0LQ
Formula:	C32H30N3O2
Molecular weight:	488.599 g/mol
DrugBank ID:	-
Buried Surface Area:	69.94 %
Polar Surface area:	57.23 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	1
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-16.4416	-20.7724	5.58095

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
C10	CD2	LEU- 23	3.8	0	Hydrophobic	false
C30	CD2	LEU- 23	3.73	0	Hydrophobic	false
N3	OD1	ASP- 25	2.82	124.35	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 25	2.77	159.36	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 25	2.67	157.35	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 25	2.96	128.42	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 25	2.82	0	Ionic (Ligand Cationic)	false
N3	OD2	ASP- 25	2.77	0	Ionic (Ligand Cationic)	false
N3	OD1	ASP- 25	2.67	0	Ionic (Ligand Cationic)	false
N3	OD2	ASP- 25	2.96	0	Ionic (Ligand Cationic)	false
C25	CB	ALA- 28	3.65	0	Hydrophobic	false
C13	CB	ALA- 28	3.73	0	Hydrophobic	false
C15	CB	ASP- 29	3.99	0	Hydrophobic	false
C14	CB	ASP- 30	4.42	0	Hydrophobic	false
C13	CG2	VAL- 32	4.26	0	Hydrophobic	false
C24	CG2	VAL- 32	3.99	0	Hydrophobic	false
C24	CD1	ILE- 47	4.14	0	Hydrophobic	false
O1	N	ILE- 50	3.08	141.44	H-Bond (Protein Donor)	false
O1	N	ILE- 50	3.02	165.25	H-Bond (Protein Donor)	false
C28	CG1	ILE- 50	4.4	0	Hydrophobic	false
C13	CD1	ILE- 50	4.14	0	Hydrophobic	false
C21	CG2	ILE- 50	4.19	0	Hydrophobic	false
C25	CD1	ILE- 50	3.57	0	Hydrophobic	false
C8	CG	PRO- 81	4.03	0	Hydrophobic	false
C29	CG	PRO- 81	3.4	0	Hydrophobic	false
C30	CB	VAL- 82	4.02	0	Hydrophobic	false
C9	CB	VAL- 82	3.59	0	Hydrophobic	false
C9	CD1	ILE- 84	4.07	0	Hydrophobic	false
C12	CD1	ILE- 84	4.05	0	Hydrophobic	false
C25	CD1	ILE- 84	3.98	0	Hydrophobic	false
C29	CG2	ILE- 84	3.79	0	Hydrophobic	false