scPDB - 4jtz entry

Protein Data Bank Entry:

PDB ID : 4jtz

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2013-03-24

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_HCVJ4
AC:	O92972
Organism:	Hepatitis C virus genotype 1b
Reign:	Viruses
TaxID:	420174
EC Number:	2.7.7.48

Chains:

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

Ligand binding site composition:

B-Factor:	47.237
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.037	509.625

% Hydrophobic	% Polar
60.93	39.07
According to VolSite

Ligand :

HET Code:	1NW
Formula:	C28H16F6N4O3
Molecular weight:	570.442 g/mol
DrugBank ID:	-
Buried Surface Area:	55.61 %
Polar Surface area:	83.89 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-22.6703	52.7186	54.3541

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
F29	CD2	LEU- 419	3.25	0	Hydrophobic	false
C14	CD2	LEU- 419	3.86	0	Hydrophobic	false
C16	CD1	LEU- 419	3.8	0	Hydrophobic	false
C4	CD1	LEU- 419	4.02	0	Hydrophobic	false
C3	CB	ARG- 422	4.45	0	Hydrophobic	false
F28	CD	ARG- 422	4.22	0	Hydrophobic	false
F19	SD	MET- 423	3.71	0	Hydrophobic	false
C27	CE	MET- 423	4.28	0	Hydrophobic	false
F32	SD	MET- 423	4.48	0	Hydrophobic	false
F28	CB	MET- 423	3.99	0	Hydrophobic	false
F31	CB	HIS- 475	3.57	0	Hydrophobic	false
N8	N	SER- 476	2.81	141.27	H-Bond (Protein Donor)	false
O18	N	TYR- 477	3.34	121.33	H-Bond (Protein Donor)	false
F31	CE1	TYR- 477	3.72	0	Hydrophobic	false
C13	CD1	ILE- 482	3.78	0	Hydrophobic	false
C14	CG2	ILE- 482	4.22	0	Hydrophobic	false
F29	CG2	ILE- 482	4.07	0	Hydrophobic	false
C21	CG2	ILE- 482	3.64	0	Hydrophobic	false
F30	CG1	VAL- 485	3.58	0	Hydrophobic	false
F30	CB	ALA- 486	4.07	0	Hydrophobic	false
F19	CD1	LEU- 489	4.42	0	Hydrophobic	false
N38	NE	ARG- 490	3.27	159.55	H-Bond (Protein Donor)	false
C41	CB	PRO- 496	3.5	0	Hydrophobic	false
F19	CB	LEU- 497	3.76	0	Hydrophobic	false
F32	CD1	LEU- 497	3.37	0	Hydrophobic	false
C15	CD2	LEU- 497	3.46	0	Hydrophobic	false
C25	CB	LEU- 497	3.94	0	Hydrophobic	false
C23	CD2	LEU- 497	3.83	0	Hydrophobic	false
O34	N	LEU- 497	2.97	163.33	H-Bond (Protein Donor)	false
F28	CD2	TRP- 528	3.46	0	Hydrophobic	false
F32	CE3	TRP- 528	3.85	0	Hydrophobic	false
C4	CE3	TRP- 528	3.1	0	Hydrophobic	false
C2	CB	TRP- 528	3.72	0	Hydrophobic	false