scPDB - 2o5d entry

Protein Data Bank Entry:

PDB ID : 2o5d

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2006-12-05

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:	34.269
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.302	340.875

% Hydrophobic	% Polar
64.36	35.64
According to VolSite

Ligand :

HET Code:	VR1
Formula:	C24H20FN4O7S2
Molecular weight:	559.567 g/mol
DrugBank ID:	-
Buried Surface Area:	51.81 %
Polar Surface area:	198.95 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-6.46261	34.9365	-34.4187

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
S13	CD1	LEU- 419	3.75	0	Hydrophobic	false
C24	CD1	LEU- 419	3.7	0	Hydrophobic	false
C25	CD1	LEU- 419	3.74	0	Hydrophobic	false
C23	CD	ARG- 422	4.3	0	Hydrophobic	false
F	CB	ARG- 422	3.44	0	Hydrophobic	false
F	CB	MET- 423	3.99	0	Hydrophobic	false
C31	CB	HIS- 475	4.39	0	Hydrophobic	false
N11	N	SER- 476	2.94	135.55	H-Bond (Protein Donor)	false
O14	N	TYR- 477	2.82	135.01	H-Bond (Protein Donor)	false
C6	CG2	ILE- 482	4.3	0	Hydrophobic	false
C7	CG1	VAL- 485	3.82	0	Hydrophobic	false
C7	CB	ALA- 486	3.51	0	Hydrophobic	false
C7	CD1	LEU- 489	4.34	0	Hydrophobic	false
C25	CD1	LEU- 497	3.83	0	Hydrophobic	false
F	CD2	TRP- 528	3.63	0	Hydrophobic	false
C25	CE3	TRP- 528	3.39	0	Hydrophobic	false
C23	CB	TRP- 528	4.1	0	Hydrophobic	false
O28	NZ	LYS- 533	2.63	132.66	H-Bond (Protein Donor)	false
O29	NZ	LYS- 533	2.77	123.24	H-Bond (Protein Donor)	false