scPDB - 2vg5 entry

Protein Data Bank Entry:

PDB ID : 2vg5

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2007-11-08

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:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	86 %
B	14 %

Ligand binding site composition:

B-Factor:	33.793
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.786	408.375

% Hydrophobic	% Polar
77.69	22.31
According to VolSite

Ligand :

HET Code:	NNC
Formula:	C17H13ClN2O3S
Molecular weight:	360.815 g/mol
DrugBank ID:	DB08282
Buried Surface Area:	78.81 %
Polar Surface area:	90.73 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
11.258	14.8573	16.9028

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
C6	CG	PRO- 95	3.76	0	Hydrophobic	false
C10	CD2	LEU- 100	3.87	0	Hydrophobic	false
C17	CD1	LEU- 100	4.2	0	Hydrophobic	false
C1	CD2	LEU- 100	4.05	0	Hydrophobic	false
C13	CD1	LEU- 100	3.99	0	Hydrophobic	false
N2	O	LYS- 101	2.66	174.32	H-Bond (Ligand Donor)	false
C12	CG	LYS- 103	3.65	0	Hydrophobic	false
C14	CG1	VAL- 106	4.16	0	Hydrophobic	false
CL2	CG1	VAL- 106	3.39	0	Hydrophobic	false
C15	CG2	VAL- 106	3.69	0	Hydrophobic	false
C10	CB	VAL- 179	3.96	0	Hydrophobic	false
C1	CB	TYR- 181	3.37	0	Hydrophobic	false
C3	CB	TYR- 188	3.61	0	Hydrophobic	false
CL2	CD2	PHE- 227	3.63	0	Hydrophobic	false
C5	CE3	TRP- 229	3.49	0	Hydrophobic	false
CL2	CB	LEU- 234	3.87	0	Hydrophobic	false
C4	CD1	LEU- 234	3.39	0	Hydrophobic	false