scPDB - 3zps entry

Protein Data Bank Entry:

PDB ID : 3zps

Resolution :1.550 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:	11.505
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.049	968.625

% Hydrophobic	% Polar
42.86	57.14
According to VolSite

Ligand :

HET Code:	EQM
Formula:	C36H52BrN5O6
Molecular weight:	730.732 g/mol
DrugBank ID:	-
Buried Surface Area:	60.66 %
Polar Surface area:	149.09 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
12.6513	22.5474	5.77296

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	4.19	0	Hydrophobic	false
C5	CB	ALA- 28	3.23	0	Hydrophobic	false
O6	N	ASP- 29	2.94	175.32	H-Bond (Protein Donor)	false
C6	CB	ILE- 47	3.69	0	Hydrophobic	false
N5	O	GLY- 48	3.03	153.9	H-Bond (Ligand Donor)	false
C16	CB	ILE- 50	3.76	0	Hydrophobic	false
C17	CG1	ILE- 50	4.18	0	Hydrophobic	false
C21	CG	PRO- 81	3.79	0	Hydrophobic	false
BR	CB	PRO- 81	3.84	0	Hydrophobic	false
C24	CG2	THR- 82	3.9	0	Hydrophobic	false
C9	CG2	VAL- 84	4.33	0	Hydrophobic	false
C10	CG2	VAL- 84	4.42	0	Hydrophobic	false
C27	CD2	LEU- 123	3.38	0	Hydrophobic	false
O1	OD2	ASP- 125	3.3	150.42	H-Bond (Ligand Donor)	false
N3	O	GLY- 127	2.99	161.5	H-Bond (Ligand Donor)	false
C17	CB	ALA- 128	3.86	0	Hydrophobic	false
O4	N	ASP- 129	2.94	174.58	H-Bond (Protein Donor)	false
C19	CB	ASP- 129	4.38	0	Hydrophobic	false
C15	CD1	ILE- 147	4.41	0	Hydrophobic	false
C16	CD1	ILE- 147	4.01	0	Hydrophobic	false
N4	O	GLY- 148	2.79	169.3	H-Bond (Ligand Donor)	false
C8	CG1	ILE- 150	4.13	0	Hydrophobic	false
C35	CG1	ILE- 150	3.46	0	Hydrophobic	false
C20	CD1	ILE- 150	3.69	0	Hydrophobic	false
BR	CZ	PHE- 153	4.19	0	Hydrophobic	false
C29	CB	PRO- 181	4.47	0	Hydrophobic	false
C30	CG	PRO- 181	3.76	0	Hydrophobic	false
C29	CG2	THR- 182	4.23	0	Hydrophobic	false
C25	CG1	VAL- 184	4.48	0	Hydrophobic	false