scPDB - 3drp entry

Protein Data Bank Entry:

PDB ID : 3drp

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2008-07-11

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	100 %

Ligand binding site composition:

B-Factor:	56.898
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.597	597.375

% Hydrophobic	% Polar
70.62	29.38
According to VolSite

Ligand :

HET Code:	R8E
Formula:	C20H13Cl2N5O2
Molecular weight:	426.256 g/mol
DrugBank ID:	DB08460
Buried Surface Area:	77.78 %
Polar Surface area:	109.84 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
8.74338	11.6974	16.6343

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
CL28	CB	PRO- 95	3.87	0	Hydrophobic	false
CL28	CD1	LEU- 100	4.16	0	Hydrophobic	false
C11	CB	LEU- 100	4.38	0	Hydrophobic	false
C15	CB	LEU- 100	3.99	0	Hydrophobic	false
C5	CD1	LEU- 100	4.06	0	Hydrophobic	false
C9	CD1	LEU- 100	3.97	0	Hydrophobic	false
N20	N	LYS- 103	2.8	171.66	H-Bond (Protein Donor)	false
N19	O	LYS- 103	2.8	135.37	H-Bond (Ligand Donor)	false
C12	CB	LYS- 103	4.33	0	Hydrophobic	false
CL29	CB	VAL- 106	4.4	0	Hydrophobic	false
C17	CG1	VAL- 106	3.93	0	Hydrophobic	false
C22	CG2	VAL- 106	4.19	0	Hydrophobic	false
C13	CG1	VAL- 106	3.85	0	Hydrophobic	false
C12	CG1	VAL- 179	3.9	0	Hydrophobic	false
CL29	CE2	TYR- 181	3.43	0	Hydrophobic	false
CL29	CB	TYR- 188	3.81	0	Hydrophobic	false
CL28	CD1	TYR- 188	4.15	0	Hydrophobic	false
C4	CB	TYR- 188	3.21	0	Hydrophobic	false
DuAr	DuAr	TYR- 188	3.85	0	Aromatic Face/Face	false
CL28	CH2	TRP- 229	3.71	0	Hydrophobic	false
C2	CD1	LEU- 234	3.65	0	Hydrophobic	false
C1	CD1	LEU- 234	3.62	0	Hydrophobic	false
C22	CB	LEU- 234	3.87	0	Hydrophobic	false
C15	CE2	TYR- 318	3.68	0	Hydrophobic	false