scPDB - 2yoj entry

Protein Data Bank Entry:

PDB ID : 2yoj

Resolution :1.760 Å

Experimental Method : X-ray

Deposition Date : 2012-10-24

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
B	100 %

Ligand binding site composition:

B-Factor:	22.433
Number of residues:	32
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.594	783.000

% Hydrophobic	% Polar
35.34	64.66
According to VolSite

Ligand :

HET Code:	8Y6
Formula:	C25H13F2N4O5
Molecular weight:	487.391 g/mol
DrugBank ID:	-
Buried Surface Area:	59.49 %
Polar Surface area:	128.76 Å2

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

Mass center Coordinates

X	Y	Z
22.9246	-0.3285	2.20514

Binding mode :

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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	0	Hydrophobic	false
F1	CZ	PHE- 193	3.79	0	Hydrophobic	false
C12	CD	ARG- 200	4.07	0	Hydrophobic	false
C6	CB	ASN- 316	4.29	0	Hydrophobic	false
C5	CB	ASP- 319	4.16	0	Hydrophobic	false
F1	CB	ASP- 319	4.34	0	Hydrophobic	false
C1	SG	CYS- 366	3.64	0	Hydrophobic	false
C2	CB	CYS- 366	3.8	0	Hydrophobic	false
C6	SG	CYS- 366	3.43	0	Hydrophobic	false
C13	CB	CYS- 366	3.37	0	Hydrophobic	false
F2	CB	SER- 368	4.13	0	Hydrophobic	false
F2	CD1	LEU- 384	3.57	0	Hydrophobic	false
C8	CE	MET- 414	3.9	0	Hydrophobic	false
N2	O	GLN- 446	2.85	164.79	H-Bond (Ligand Donor)	false
C15	CE1	TYR- 448	4.1	0	Hydrophobic	false
O2	N	TYR- 448	2.78	178.62	H-Bond (Protein Donor)	false
O4	O	HOH- 2580	2.68	179.98	H-Bond (Protein Donor)	false