scPDB - 3lkh entry

Protein Data Bank Entry:

PDB ID : 3lkh

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2010-01-27

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
B	100 %

Ligand binding site composition:

B-Factor:	33.445
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.383	934.875

% Hydrophobic	% Polar
49.82	50.18
According to VolSite

Ligand :

HET Code:	LT6
Formula:	C23H29FN2O4
Molecular weight:	416.486 g/mol
DrugBank ID:	-
Buried Surface Area:	80.44 %
Polar Surface area:	78.87 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
29.2671	0.830033	4.1048

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
C16	CD1	PHE- 193	4.39	0	Hydrophobic	false
O1	O	TYR- 195	2.65	159.8	H-Bond (Ligand Donor)	false
C21	CB	SER- 196	3.87	0	Hydrophobic	false
C10	CG	PRO- 197	3.84	0	Hydrophobic	false
C11	CB	PRO- 197	4.49	0	Hydrophobic	false
C14	CG	PRO- 197	4.08	0	Hydrophobic	false
C14	CD	ARG- 200	4.18	0	Hydrophobic	false
C7	CB	CYS- 366	4.21	0	Hydrophobic	false
C6	CB	SER- 368	4.08	0	Hydrophobic	false
C6	CD1	LEU- 384	3.64	0	Hydrophobic	false
C10	CG	MET- 414	3.73	0	Hydrophobic	false
C11	CB	MET- 414	3.99	0	Hydrophobic	false
C8	CE	MET- 414	3.73	0	Hydrophobic	false
C9	CE	MET- 414	3.54	0	Hydrophobic	false
C3	CD1	ILE- 447	4	0	Hydrophobic	false
C12	CZ	TYR- 448	4.27	0	Hydrophobic	false
C3	CZ	TYR- 452	4.02	0	Hydrophobic	false
F1	CD1	LEU- 466	3.22	0	Hydrophobic	false
C1	CB	TRP- 550	4.42	0	Hydrophobic	false
F1	CE3	TRP- 550	3.57	0	Hydrophobic	false
C3	CE2	TRP- 550	3.76	0	Hydrophobic	false
C20	CB	TRP- 550	4.03	0	Hydrophobic	false
F1	CZ	PHE- 551	3.61	0	Hydrophobic	false
C16	CB	TYR- 555	3.93	0	Hydrophobic	false
C1	CB	TYR- 555	4.04	0	Hydrophobic	false
O1	O	HOH- 659	2.99	179.97	H-Bond (Protein Donor)	false