scPDB - 4mkb entry

Protein Data Bank Entry:

PDB ID : 4mkb

Resolution :1.900 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
A	100 %

Ligand binding site composition:

B-Factor:	21.010
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.361	2257.875

% Hydrophobic	% Polar
38.57	61.43
According to VolSite

Ligand :

HET Code:	28V
Formula:	C24H27N3O4S
Molecular weight:	453.554 g/mol
DrugBank ID:	-
Buried Surface Area:	61.69 %
Polar Surface area:	105.24 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-9.03981	8.68872	9.74937

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
C28	CG	PRO- 197	4.1	0	Hydrophobic	false
C29	CG	PRO- 197	4.22	0	Hydrophobic	false
C29	CD	ARG- 200	3.69	0	Hydrophobic	false
C30	CD	ARG- 200	4.34	0	Hydrophobic	false
C32	CD	ARG- 200	4.32	0	Hydrophobic	false
O2	ND2	ASN- 291	2.9	173.25	H-Bond (Protein Donor)	false
C9	CB	ASN- 316	4.11	0	Hydrophobic	false
O2	N	ASP- 318	3.29	138.27	H-Bond (Protein Donor)	false
N4	OD1	ASP- 318	2.94	165.38	H-Bond (Ligand Donor)	false
C10	CB	ASP- 319	4.29	0	Hydrophobic	false
C9	SG	CYS- 366	4.12	0	Hydrophobic	false
C30	CB	CYS- 366	4.32	0	Hydrophobic	false
C32	SG	CYS- 366	3.64	0	Hydrophobic	false
C14	CB	CYS- 366	4	0	Hydrophobic	false
C30	CB	SER- 368	3.67	0	Hydrophobic	false
C29	CD1	LEU- 384	3.96	0	Hydrophobic	false
C28	CB	MET- 414	4.4	0	Hydrophobic	false
C29	CE	MET- 414	4.47	0	Hydrophobic	false
C16	CE	MET- 414	3.73	0	Hydrophobic	false
C28	CZ	TYR- 415	3.73	0	Hydrophobic	false
N22	O	GLN- 446	2.78	166.74	H-Bond (Ligand Donor)	false
O21	N	TYR- 448	2.85	174.41	H-Bond (Protein Donor)	false
C29	CE1	TYR- 448	4.36	0	Hydrophobic	false
C32	CE1	TYR- 448	3.62	0	Hydrophobic	false
C6	CB	SER- 556	3.96	0	Hydrophobic	false
C33	CB	SER- 556	3.7	0	Hydrophobic	false