scPDB - 1vru entry

Protein Data Bank Entry:

PDB ID : 1vru

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1995-04-19

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	86 %
B	14 %

Ligand binding site composition:

B-Factor:	35.950
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.601	486.000

% Hydrophobic	% Polar
76.39	23.61
According to VolSite

Ligand :

HET Code:	AAP
Formula:	C17H16Cl2N2O2
Molecular weight:	351.227 g/mol
DrugBank ID:	DB07332
Buried Surface Area:	78.14 %
Polar Surface area:	72.19 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
2.23613	-36.8553	22.1314

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
C3'	CB	PRO- 95	4.26	0	Hydrophobic	false
CM'	CB	PRO- 95	4.08	0	Hydrophobic	false
C3	CB	LEU- 100	3.95	0	Hydrophobic	false
CL2	CB	LEU- 100	4.38	0	Hydrophobic	false
CM'	CD2	LEU- 100	3.48	0	Hydrophobic	false
C4	CD1	LEU- 100	4.14	0	Hydrophobic	false
C1'	CD1	LEU- 100	3.98	0	Hydrophobic	false
C2'	CD2	LEU- 100	3.92	0	Hydrophobic	false
C1	CD1	LEU- 100	3.93	0	Hydrophobic	false
C2	CG	LYS- 103	3.95	0	Hydrophobic	false
C5	CG2	VAL- 106	4.27	0	Hydrophobic	false
CL6	CG1	VAL- 106	3.79	0	Hydrophobic	false
CM'	CG	GLU- 138	3.59	0	Hydrophobic	false
N	O	VAL- 179	3.19	166.02	H-Bond (Ligand Donor)	false
CL2	CG1	VAL- 179	4.05	0	Hydrophobic	false
CM'	CD1	TYR- 181	3.68	0	Hydrophobic	false
C3'	CD2	TYR- 181	3.3	0	Hydrophobic	false
C2'	CB	TYR- 181	3.68	0	Hydrophobic	false
CA	CB	TYR- 188	3.81	0	Hydrophobic	false
CL6	CD2	TYR- 188	3.89	0	Hydrophobic	false
CM5	CE2	TYR- 188	3.67	0	Hydrophobic	false
C6'	CB	TYR- 188	4.05	0	Hydrophobic	false
CL6	CD2	PHE- 227	4.09	0	Hydrophobic	false
CM5	CD2	TRP- 229	3.69	0	Hydrophobic	false
CL6	CD1	LEU- 234	4.42	0	Hydrophobic	false
CM5	CD1	LEU- 234	3.38	0	Hydrophobic	false