scPDB - 3mf5 entry

Protein Data Bank Entry:

PDB ID : 3mf5

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-04-01

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:	25.296
Number of residues:	23
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.770	327.375

% Hydrophobic	% Polar
72.16	27.84
According to VolSite

Ligand :

HET Code:	HJZ
Formula:	C24H23O2S
Molecular weight:	375.503 g/mol
DrugBank ID:	-
Buried Surface Area:	58.23 %
Polar Surface area:	68.36 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	0
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
76.761	33.8975	-10

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
S1	CD1	LEU- 419	3.95	0	Hydrophobic	false
C16	CD1	LEU- 419	4.15	0	Hydrophobic	false
C6	CD2	LEU- 419	3.9	0	Hydrophobic	false
C25	CD1	LEU- 419	3.96	0	Hydrophobic	false
C23	CD1	LEU- 419	4.04	0	Hydrophobic	false
C27	CB	ARG- 422	3.55	0	Hydrophobic	false
C16	SD	MET- 423	3.91	0	Hydrophobic	false
C25	CB	MET- 423	4.19	0	Hydrophobic	false
C27	CB	MET- 423	3.86	0	Hydrophobic	false
C19	CE	MET- 423	3.59	0	Hydrophobic	false
O10	N	SER- 476	2.91	136.31	H-Bond (Protein Donor)	false
O9	N	TYR- 477	2.78	159.01	H-Bond (Protein Donor)	false
C23	CE1	TYR- 477	3.89	0	Hydrophobic	false
S1	CG1	ILE- 482	3.57	0	Hydrophobic	false
C20	CG2	ILE- 482	3.42	0	Hydrophobic	false
C17	CG1	VAL- 485	4.49	0	Hydrophobic	false
C18	CB	ALA- 486	3.93	0	Hydrophobic	false
C17	CD1	LEU- 489	4.47	0	Hydrophobic	false
C16	CB	LEU- 497	3.89	0	Hydrophobic	false
C26	CD1	LEU- 497	3.64	0	Hydrophobic	false
C23	CB	TRP- 528	4.24	0	Hydrophobic	false
C27	CD2	TRP- 528	3.49	0	Hydrophobic	false
C24	CE3	TRP- 528	3.45	0	Hydrophobic	false