scPDB - 3vqs entry

Protein Data Bank Entry:

PDB ID : 3vqs

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-03-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Genome polyprotein
ID:	POLG_HCVBK
AC:	P26663
Organism:	Hepatitis C virus genotype 1b
Reign:	Viruses
TaxID:	11105
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	34.185
Number of residues:	51
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.777	1768.500

% Hydrophobic	% Polar
44.85	55.15
According to VolSite

Ligand :

HET Code:	JT1
Formula:	C28H23F7N6O4S2
Molecular weight:	704.639 g/mol
DrugBank ID:	DB13095
Buried Surface Area:	77.62 %
Polar Surface area:	154.23 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-3.02455	85.1354	45.2176

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
C45	CB	VAL- 179	3.92	0	Hydrophobic	false
C46	CZ	TYR- 191	4.36	0	Hydrophobic	false
S27	CD2	PHE- 193	3.85	0	Hydrophobic	false
C30	CB	PHE- 193	4.32	0	Hydrophobic	false
C46	CD1	PHE- 193	4.11	0	Hydrophobic	false
DuAr	DuAr	PHE- 193	3.91	0	Aromatic Face/Face	false
N18	O	TYR- 195	3.01	133.73	H-Bond (Ligand Donor)	false
C24	CG	PRO- 197	4.35	0	Hydrophobic	false
F38	CG	PRO- 197	3.62	0	Hydrophobic	false
F47	CB	PRO- 197	3.59	0	Hydrophobic	false
C24	CD	ARG- 200	3.31	0	Hydrophobic	false
N32	OG	SER- 288	2.94	174.11	H-Bond (Protein Donor)	false
C46	CB	SER- 288	4.16	0	Hydrophobic	false
C46	CB	CYS- 289	3.85	0	Hydrophobic	false
C21	SG	CYS- 366	4.49	0	Hydrophobic	false
C22	CB	CYS- 366	3.85	0	Hydrophobic	false
F37	CB	SER- 368	3.3	0	Hydrophobic	false
F47	CD1	LEU- 384	3.5	0	Hydrophobic	false
F37	CD1	LEU- 384	3.59	0	Hydrophobic	false
F41	CD1	ILE- 413	4.38	0	Hydrophobic	false
F42	CG2	ILE- 413	4.22	0	Hydrophobic	false
C10	CG2	ILE- 413	3.82	0	Hydrophobic	false
C11	SD	MET- 414	3.72	0	Hydrophobic	false
C12	CE	MET- 414	4.4	0	Hydrophobic	false
C24	CE	MET- 414	3.81	0	Hydrophobic	false
F38	CE	MET- 414	3.77	0	Hydrophobic	false
C24	CE	MET- 414	3.81	0	Hydrophobic	false
F37	CE2	TYR- 415	3.32	0	Hydrophobic	false
F38	CE2	TYR- 415	4.28	0	Hydrophobic	false
F39	CZ	TYR- 415	3.6	0	Hydrophobic	false
F41	CD1	ILE- 447	4.28	0	Hydrophobic	false
C10	CD1	ILE- 447	3.56	0	Hydrophobic	false
C12	CG2	ILE- 447	4.08	0	Hydrophobic	false
S27	CB	TYR- 448	3.78	0	Hydrophobic	false
F39	CE1	TYR- 448	4.19	0	Hydrophobic	false
C13	CB	ALA- 450	4.24	0	Hydrophobic	false
S27	CB	ALA- 450	3.91	0	Hydrophobic	false
F41	CG	TYR- 452	3.33	0	Hydrophobic	false
F43	CE2	TYR- 452	3.26	0	Hydrophobic	false
F41	CD1	ILE- 454	3.34	0	Hydrophobic	false
F42	CG2	ILE- 462	3.32	0	Hydrophobic	false
F42	CD1	LEU- 466	4.09	0	Hydrophobic	false
C4	CD2	LEU- 466	3.84	0	Hydrophobic	false
C10	CD1	LEU- 466	3.82	0	Hydrophobic	false
F42	CD2	LEU- 547	4.04	0	Hydrophobic	false
F43	CD2	LEU- 547	4.2	0	Hydrophobic	false
C8	CD1	LEU- 547	3.83	0	Hydrophobic	false
F43	CB	TRP- 550	4.44	0	Hydrophobic	false
C30	CB	TYR- 555	4.09	0	Hydrophobic	false
C45	CD1	TYR- 555	3.36	0	Hydrophobic	false
C14	CB	SER- 556	4.06	0	Hydrophobic	false