scPDB - 3lp2 entry

Protein Data Bank Entry:

PDB ID : 3lp2

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2010-02-04

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_HV1H2
AC:	P04585
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11706
EC Number:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
B	4 %

Ligand binding site composition:

B-Factor:	77.406
Number of residues:	23
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.456	313.875

% Hydrophobic	% Polar
62.37	37.63
According to VolSite

Ligand :

HET Code:	LP9
Formula:	C21H21N3O6
Molecular weight:	411.408 g/mol
DrugBank ID:	-
Buried Surface Area:	57.46 %
Polar Surface area:	118.09 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	0
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
9.58317	9.6313	25.5002

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
C22	CD1	LEU- 100	3.83	0	Hydrophobic	false
C1	CG1	VAL- 108	3.51	0	Hydrophobic	false
C14	CG2	VAL- 108	3.62	0	Hydrophobic	false
C22	CB	TYR- 181	3.88	0	Hydrophobic	false
C24	CB	TYR- 181	3.7	0	Hydrophobic	false
C24	CB	TYR- 183	3.91	0	Hydrophobic	false
C18	CB	ASP- 186	4.12	0	Hydrophobic	false
C21	CD1	TYR- 188	4.26	0	Hydrophobic	false
C22	CG	TYR- 188	3.54	0	Hydrophobic	false
C24	CB	TYR- 188	4.07	0	Hydrophobic	false
C18	CB	TYR- 188	3.67	0	Hydrophobic	false
DuAr	NZ	LYS- 223	3.35	176.89	Pi/Cation	false
C4	CG	LYS- 223	4.19	0	Hydrophobic	false
C8	CG	LYS- 223	3.67	0	Hydrophobic	false
C26	CG	LYS- 223	4.09	0	Hydrophobic	false
C15	CB	PHE- 227	4.08	0	Hydrophobic	false
C	CB	PHE- 227	3.45	0	Hydrophobic	false
O	N	LEU- 228	3.35	146.1	H-Bond (Protein Donor)	false
C7	CB	LEU- 228	4.28	0	Hydrophobic	false
C26	CD2	LEU- 228	4.19	0	Hydrophobic	false
C1	CB	TRP- 229	4.5	0	Hydrophobic	false
C21	CH2	TRP- 229	3.99	0	Hydrophobic	false
C23	CZ2	TRP- 229	3.5	0	Hydrophobic	false
C15	CB	TRP- 229	3.45	0	Hydrophobic	false
C16	CD1	LEU- 234	3.59	0	Hydrophobic	false