scPDB - 1vik entry

Protein Data Bank Entry:

PDB ID : 1vik

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1997-05-07

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_HV1Z2
AC:	P12499
Organism:	Human immunodeficiency virus type 1 group M subtype D
Reign:	Viruses
TaxID:	11683
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	48 %
B	52 %

Ligand binding site composition:

B-Factor:	8.327
Number of residues:	47
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.127	931.500

% Hydrophobic	% Polar
43.48	56.52
According to VolSite

Ligand :

HET Code:	BAY
Formula:	C64H82N4O10S2
Molecular weight:	1131.487 g/mol
DrugBank ID:	-
Buried Surface Area:	55.87 %
Polar Surface area:	241.89 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	6
Rings:	6
Aromatic rings:	6
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	4
Rotatable Bonds:	27

Mass center Coordinates

X	Y	Z
12.659	22.0973	5.74791

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
C18	CD	ARG- 8	3.99	0	Hydrophobic	false
C18	CD1	LEU- 23	4.37	0	Hydrophobic	false
C50	CD2	LEU- 23	4.47	0	Hydrophobic	false
O42	OD1	ASP- 25	2.94	131.4	H-Bond (Ligand Donor)	false
O42	OD2	ASP- 25	2.81	162.38	H-Bond (Ligand Donor)	false
N51	O	GLY- 27	2.98	169.16	H-Bond (Ligand Donor)	false
C27	CB	ALA- 28	4.11	0	Hydrophobic	false
C56	CB	ALA- 28	4.44	0	Hydrophobic	false
C1	CB	ASP- 29	4.35	0	Hydrophobic	false
C73	CB	ASP- 29	4.48	0	Hydrophobic	false
O22	N	ASP- 29	3.35	165.33	H-Bond (Protein Donor)	false
O60	N	ASP- 29	2.97	165.56	H-Bond (Protein Donor)	false
C56	CG2	VAL- 32	4.16	0	Hydrophobic	false
C57	CG2	VAL- 32	4.18	0	Hydrophobic	false
C1	CG2	ILE- 47	4.36	0	Hydrophobic	false
C3	CG2	ILE- 47	4.5	0	Hydrophobic	false
C26	CD1	ILE- 47	3.88	0	Hydrophobic	false
C57	CD1	ILE- 47	3.75	0	Hydrophobic	false
C80	CG2	ILE- 47	4.3	0	Hydrophobic	false
O7	N	GLY- 48	3.01	157.83	H-Bond (Protein Donor)	false
O75	N	GLY- 48	2.51	166.95	H-Bond (Protein Donor)	false
N23	O	GLY- 48	2.87	159.49	H-Bond (Ligand Donor)	false
N58	O	GLY- 48	2.87	145.94	H-Bond (Ligand Donor)	false
C27	CG1	ILE- 50	3.95	0	Hydrophobic	false
C35	CD1	ILE- 50	3.45	0	Hydrophobic	false
C56	CG1	ILE- 50	3.84	0	Hydrophobic	false
C16	CB	PRO- 81	3.38	0	Hydrophobic	false
C17	CG	PRO- 81	4.3	0	Hydrophobic	false
C37	CG	PRO- 81	3.97	0	Hydrophobic	false
C48	CG	PRO- 81	4.01	0	Hydrophobic	false
C69	CG	PRO- 81	3.89	0	Hydrophobic	false
C15	CG	PRO- 81	3.38	0	Hydrophobic	false
C16	CG1	VAL- 82	3.92	0	Hydrophobic	false
C47	CG1	VAL- 82	3.72	0	Hydrophobic	false
C17	CG2	VAL- 82	3.26	0	Hydrophobic	false
C49	CG1	VAL- 82	3.36	0	Hydrophobic	false
C27	CD1	ILE- 84	4.06	0	Hydrophobic	false
C34	CD1	ILE- 84	3.8	0	Hydrophobic	false
C46	CD1	ILE- 84	3.37	0	Hydrophobic	false
O53	O	HOH- 202	2.85	179.95	H-Bond (Protein Donor)	false