scPDB - 4mk8 entry

Protein Data Bank Entry:

PDB ID : 4mk8

Resolution :2.090 Å

Experimental Method : X-ray

Deposition Date : 2013-09-04

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:	2.7.7.48

Chains:

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

Ligand binding site composition:

B-Factor:	20.076
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.860	897.750

% Hydrophobic	% Polar
37.97	62.03
According to VolSite

Ligand :

HET Code:	28Q
Formula:	C25H30N2O4S
Molecular weight:	454.582 g/mol
DrugBank ID:	-
Buried Surface Area:	62.91 %
Polar Surface area:	92.88 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-8.99106	8.64816	-13.7868

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
C15	CE1	PHE- 193	4.17	0	Hydrophobic	false
C31	CB	PRO- 197	4.18	0	Hydrophobic	false
C32	CB	PRO- 197	4.11	0	Hydrophobic	false
C32	CD	ARG- 200	3.65	0	Hydrophobic	false
C33	CD	ARG- 200	4.35	0	Hydrophobic	false
O25	ND2	ASN- 291	2.82	166.11	H-Bond (Protein Donor)	false
C18	CB	ASN- 316	4.36	0	Hydrophobic	false
N23	OD1	ASP- 318	2.8	159.99	H-Bond (Ligand Donor)	false
C19	CB	ASP- 319	3.67	0	Hydrophobic	false
C18	SG	CYS- 366	4.35	0	Hydrophobic	false
C33	CB	SER- 368	3.94	0	Hydrophobic	false
C32	CD1	LEU- 384	3.81	0	Hydrophobic	false
C31	CB	MET- 414	4.36	0	Hydrophobic	false
C1	CE	MET- 414	3.73	0	Hydrophobic	false
C31	CZ	TYR- 415	3.67	0	Hydrophobic	false
C33	CZ	TYR- 415	4.46	0	Hydrophobic	false
N11	O	GLN- 446	2.81	166.57	H-Bond (Ligand Donor)	false
O14	N	TYR- 448	2.84	164.9	H-Bond (Protein Donor)	false
C15	CD1	TYR- 448	3.95	0	Hydrophobic	false
C21	CB	SER- 556	4.43	0	Hydrophobic	false
C27	CB	SER- 556	3.47	0	Hydrophobic	false