scPDB - 3upi entry

Protein Data Bank Entry:

PDB ID : 3upi

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2011-11-18

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
A	100 %

Ligand binding site composition:

B-Factor:	32.326
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.855	837.000

% Hydrophobic	% Polar
39.11	60.89
According to VolSite

Ligand :

HET Code:	0C2
Formula:	C25H21F2N3O5S
Molecular weight:	513.513 g/mol
DrugBank ID:	-
Buried Surface Area:	63.48 %
Polar Surface area:	114.88 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
25.011	44.3578	44.7019

Binding mode :

What is Poseview ?

2D View
3D View

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
C25	CE1	PHE- 193	3.9	0	Hydrophobic	false
F2	CZ	PHE- 193	3.35	0	Hydrophobic	false
C23	CB	PRO- 197	3.66	0	Hydrophobic	false
C23	CD	ARG- 200	4.22	0	Hydrophobic	false
C1	CD	ARG- 200	3.59	0	Hydrophobic	false
C13	CB	ASN- 316	3.95	0	Hydrophobic	false
C4	CB	ASP- 319	3.65	0	Hydrophobic	false
C2	CB	CYS- 366	3.41	0	Hydrophobic	false
C5	CB	CYS- 366	3.52	0	Hydrophobic	false
C9	SG	CYS- 366	3.49	0	Hydrophobic	false
F1	CB	SER- 367	3.45	0	Hydrophobic	false
C23	CD1	LEU- 384	3.57	0	Hydrophobic	false
C21	CB	MET- 414	3.7	0	Hydrophobic	false
C11	CE	MET- 414	3.7	0	Hydrophobic	false
C21	CZ	TYR- 415	3.59	0	Hydrophobic	false
C22	CE1	TYR- 415	4.33	0	Hydrophobic	false
N2	O	GLN- 446	2.91	168.93	H-Bond (Ligand Donor)	false
C25	CD1	TYR- 448	4.21	0	Hydrophobic	false
O1	N	TYR- 448	2.76	174.92	H-Bond (Protein Donor)	false
C24	CB	SER- 556	4.4	0	Hydrophobic	false