scPDB - 1ivq entry

Protein Data Bank Entry:

PDB ID : 1ivq

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 1993-03-18

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_HV2RO
AC:	P04584
Organism:	Human immunodeficiency virus type 2 subtype A
Reign:	Viruses
TaxID:	11720
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	50 %
B	50 %

Ligand binding site composition:

B-Factor:	6.235
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.146	742.500

% Hydrophobic	% Polar
45.45	54.55
According to VolSite

Ligand :

HET Code:	0PX
Formula:	C34H51N5O5
Molecular weight:	609.799 g/mol
DrugBank ID:	-
Buried Surface Area:	67.27 %
Polar Surface area:	163.5 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
-0.491545	20.0019	21.0356

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
CD1	CD2	LEU- 23	4.03	0	Hydrophobic	false
CG11	CD2	LEU- 23	3.57	0	Hydrophobic	false
OH	OD2	ASP- 25	3.03	145.95	H-Bond (Ligand Donor)	false
OH	OD1	ASP- 25	3.43	155.81	H-Bond (Ligand Donor)	false
N2	O	GLY- 27	2.93	158.56	H-Bond (Ligand Donor)	false
CB	CB	ALA- 28	3.9	0	Hydrophobic	false
C31	CB	ALA- 28	3.21	0	Hydrophobic	false
O	N	ASP- 29	3.22	156.55	H-Bond (Protein Donor)	false
OD1	N	ASP- 30	2.96	151.38	H-Bond (Protein Donor)	false
ND2	OD2	ASP- 30	3.15	156.57	H-Bond (Ligand Donor)	false
CB	CD1	ILE- 32	4.19	0	Hydrophobic	false
C51	CD1	ILE- 32	3.64	0	Hydrophobic	false
C51	CG2	VAL- 47	3.22	0	Hydrophobic	false
N	O	GLY- 48	3.12	130.6	H-Bond (Ligand Donor)	false
ND2	O	GLY- 48	3.2	164.4	H-Bond (Ligand Donor)	false
CD2	CB	ILE- 50	3.79	0	Hydrophobic	false
CE2	CG1	ILE- 50	3.91	0	Hydrophobic	false
CG2	CG1	ILE- 50	4.21	0	Hydrophobic	false
C41	CB	ILE- 50	3.84	0	Hydrophobic	false
C21	CD1	ILE- 50	4.27	0	Hydrophobic	false
CG2	CG	PRO- 81	4.49	0	Hydrophobic	false
CZ	CG	PRO- 81	3.71	0	Hydrophobic	false
C7	CG	PRO- 81	3.9	0	Hydrophobic	false
CE1	CB	ILE- 82	3.87	0	Hydrophobic	false
CG2	CG2	ILE- 82	4.06	0	Hydrophobic	false
CB	CD1	ILE- 84	3.79	0	Hydrophobic	false
C41	CD1	ILE- 84	4.47	0	Hydrophobic	false
CG1	CD1	ILE- 84	3.8	0	Hydrophobic	false
CD2	CD1	ILE- 84	4.02	0	Hydrophobic	false
CG11	CG2	ILE- 84	4.25	0	Hydrophobic	false