scPDB - 1vij entry

Protein Data Bank Entry:

PDB ID : 1vij

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	50 %
B	50 %

Ligand binding site composition:

B-Factor:	24.301
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.274	911.250

% Hydrophobic	% Polar
44.44	55.56
According to VolSite

Ligand :

HET Code:	BAY
Formula:	C64H82N4O10S2
Molecular weight:	1131.487 g/mol
DrugBank ID:	-
Buried Surface Area:	54.17 %
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
-9.19031	15.627	27.888

Binding mode :

What is Poseview ?

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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
C65	CD	ARG- 8	3.87	0	Hydrophobic	false
C44	CD2	LEU- 23	4.25	0	Hydrophobic	false
C38	CD2	LEU- 23	3.91	0	Hydrophobic	false
O40	OD2	ASP- 25	2.58	147.26	H-Bond (Ligand Donor)	false
O40	OD1	ASP- 25	3.48	138.96	H-Bond (Ligand Donor)	false
O42	OD2	ASP- 25	2.61	177.3	H-Bond (Ligand Donor)	false
N51	O	GLY- 27	3.38	148.08	H-Bond (Ligand Donor)	false
C26	CB	ALA- 28	4.19	0	Hydrophobic	false
C27	CB	ALA- 28	4.24	0	Hydrophobic	false
C56	CB	ALA- 28	4.09	0	Hydrophobic	false
O22	N	ASP- 29	3.31	167.73	H-Bond (Protein Donor)	false
O60	N	ASP- 29	3.42	160.52	H-Bond (Protein Donor)	false
C27	CG1	VAL- 32	4.1	0	Hydrophobic	false
C56	CG1	VAL- 32	4.34	0	Hydrophobic	false
C57	CG1	VAL- 32	4.34	0	Hydrophobic	false
C3	CG2	ILE- 47	4.15	0	Hydrophobic	false
C78	CG2	ILE- 47	4.15	0	Hydrophobic	false
C26	CD1	ILE- 47	4.29	0	Hydrophobic	false
C57	CD1	ILE- 47	3.88	0	Hydrophobic	false
O7	N	GLY- 48	2.55	159.35	H-Bond (Protein Donor)	false
N23	O	GLY- 48	2.8	150.47	H-Bond (Ligand Donor)	false
C27	CD1	ILE- 50	4.4	0	Hydrophobic	false
C34	CG1	ILE- 50	4.3	0	Hydrophobic	false
C35	CD1	ILE- 50	3.9	0	Hydrophobic	false
C55	CB	ILE- 50	4.48	0	Hydrophobic	false
C56	CD1	ILE- 50	4.48	0	Hydrophobic	false
C33	CD1	ILE- 50	3.76	0	Hydrophobic	false
C47	CD1	ILE- 50	3.35	0	Hydrophobic	false
C47	CG	PRO- 81	3.86	0	Hydrophobic	false
C14	CG	PRO- 81	3.66	0	Hydrophobic	false
C16	CB	PRO- 81	3.63	0	Hydrophobic	false
C35	CG	PRO- 81	3.7	0	Hydrophobic	false
C48	CG	PRO- 81	4.05	0	Hydrophobic	false
C18	CG1	VAL- 82	3.73	0	Hydrophobic	false
C50	CG2	VAL- 82	3.91	0	Hydrophobic	false
C49	CG2	VAL- 82	3.94	0	Hydrophobic	false
C66	CG1	VAL- 82	3.84	0	Hydrophobic	false
C37	CG2	VAL- 82	3.4	0	Hydrophobic	false
C27	CD1	ILE- 84	3.68	0	Hydrophobic	false
C56	CG2	ILE- 84	4.21	0	Hydrophobic	false
C33	CD1	ILE- 84	4	0	Hydrophobic	false
C46	CD1	ILE- 84	3.5	0	Hydrophobic	false