scPDB - 3zpu entry

Protein Data Bank Entry:

PDB ID : 3zpu

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2013-03-01

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_HV1B1
AC:	P03366
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11678
EC Number:	3.4.23.16

Chains:

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

Ligand binding site composition:

B-Factor:	10.520
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.050	894.375

% Hydrophobic	% Polar
41.51	58.49
According to VolSite

Ligand :

HET Code:	M8B
Formula:	C37H52BrN5O6
Molecular weight:	742.743 g/mol
DrugBank ID:	-
Buried Surface Area:	61.57 %
Polar Surface area:	149.09 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
12.6251	22.6975	5.67698

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	4.08	0	Hydrophobic	false
C6	CB	ALA- 28	3.56	0	Hydrophobic	false
O6	N	ASP- 29	2.91	178.1	H-Bond (Protein Donor)	false
C6	CB	ASP- 30	4.44	0	Hydrophobic	false
C35	CB	ILE- 47	3.67	0	Hydrophobic	false
N5	O	GLY- 48	2.89	160.68	H-Bond (Ligand Donor)	false
C17	CB	ILE- 50	3.63	0	Hydrophobic	false
C15	CG1	ILE- 50	3.99	0	Hydrophobic	false
BR1	CB	PRO- 81	3.95	0	Hydrophobic	false
C21	CG	PRO- 81	3.5	0	Hydrophobic	false
C11	CG2	THR- 82	3.72	0	Hydrophobic	false
C24	CG2	THR- 82	3.76	0	Hydrophobic	false
C10	CG2	VAL- 84	4.22	0	Hydrophobic	false
C9	CG2	VAL- 84	4.23	0	Hydrophobic	false
C28	CD2	LEU- 123	3.29	0	Hydrophobic	false
C26	CD2	LEU- 123	4.37	0	Hydrophobic	false
O1	OD2	ASP- 125	2.87	161.53	H-Bond (Ligand Donor)	false
N3	O	GLY- 127	3.08	159.99	H-Bond (Ligand Donor)	false
C15	CB	ALA- 128	3.95	0	Hydrophobic	false
C19	CB	ASP- 129	4.4	0	Hydrophobic	false
O4	N	ASP- 129	2.95	174.93	H-Bond (Protein Donor)	false
C16	CB	ASP- 130	4.4	0	Hydrophobic	false
C17	CD1	ILE- 147	4.1	0	Hydrophobic	false
N4	O	GLY- 148	2.92	168.87	H-Bond (Ligand Donor)	false
C8	CG1	ILE- 150	4.34	0	Hydrophobic	false
C5	CG1	ILE- 150	3.49	0	Hydrophobic	false
C20	CD1	ILE- 150	3.55	0	Hydrophobic	false
BR1	CZ	PHE- 153	4.24	0	Hydrophobic	false
C30	CG	PRO- 181	3.7	0	Hydrophobic	false
C32	CG2	THR- 182	4.12	0	Hydrophobic	false
C15	CG2	VAL- 184	4.37	0	Hydrophobic	false
C25	CG1	VAL- 184	4.27	0	Hydrophobic	false