scPDB - 3phe entry

Protein Data Bank Entry:

PDB ID : 3phe

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2010-11-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	RNA-directed RNA polymerase
ID:	D0PY27_9HEPC
AC:	D0PY27
Organism:	Hepatitis C virus
Reign:	Viruses
TaxID:	11103
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.088
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.302	415.125

% Hydrophobic	% Polar
56.91	43.09
According to VolSite

Ligand :

HET Code:	C9A
Formula:	C30H30ClFN3O5S
Molecular weight:	599.093 g/mol
DrugBank ID:	-
Buried Surface Area:	49.62 %
Polar Surface area:	96.81 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
32.4288	74.8833	24.6852

Binding mode :

What is Poseview ?

2D View
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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
CL39	CD2	LEU- 419	3.97	0	Hydrophobic	false
C38	CD2	LEU- 419	3.5	0	Hydrophobic	false
CL39	CB	ARG- 422	3.44	0	Hydrophobic	false
CL39	CB	MET- 423	3.73	0	Hydrophobic	false
O32	N	SER- 476	2.9	136.96	H-Bond (Protein Donor)	false
O14	N	TYR- 477	2.68	137.77	H-Bond (Protein Donor)	false
F10	CB	PRO- 479	3.67	0	Hydrophobic	false
C6	CG2	ILE- 482	3.58	0	Hydrophobic	false
C8	CG2	ILE- 482	3.86	0	Hydrophobic	false
C9	CG1	ILE- 482	3.56	0	Hydrophobic	false
C21	CG2	ILE- 482	3.98	0	Hydrophobic	false
C12	CG1	ILE- 482	3.56	0	Hydrophobic	false
C26	CG1	VAL- 485	4.39	0	Hydrophobic	false
C26	CB	ALA- 486	3.67	0	Hydrophobic	false
C26	CD1	LEU- 489	3.96	0	Hydrophobic	false
O27	N	LEU- 497	2.91	145.77	H-Bond (Protein Donor)	false
C36	CD2	LEU- 497	4.05	0	Hydrophobic	false
C37	CD1	LEU- 497	3.85	0	Hydrophobic	false
C22	CB	LEU- 497	3.73	0	Hydrophobic	false
C20	CD2	LEU- 497	3.7	0	Hydrophobic	false
CL39	CD2	TRP- 528	3.66	0	Hydrophobic	false
C37	CE3	TRP- 528	3.43	0	Hydrophobic	false
C40	CB	TRP- 528	3.72	0	Hydrophobic	false