scPDB - 2xi3 entry

Protein Data Bank Entry:

PDB ID : 2xi3

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2010-06-25

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_HCVH
AC:	P27958
Organism:	Hepatitis C virus genotype 1a
Reign:	Viruses
TaxID:	11108
EC Number:	2.7.7.48

Chains:

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

Ligand binding site composition:

B-Factor:	24.034
Number of residues:	29
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	3
Water Molecules:	0
Cofactors:	GTP
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.278	2460.375

% Hydrophobic	% Polar
30.59	69.41
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	46.9 %
Polar Surface area:	335.56 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
7.43697	0.388312	15.5151

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
O1B	NH1	ARG- 48	3.18	133.43	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 51	3.88	0	Ionic (Protein Cationic)	false
N7	NZ	LYS- 141	2.96	163.24	H-Bond (Protein Donor)	false
N1	OD2	ASP- 225	2.92	162.31	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 225	2.93	174.44	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 318	2.72	164.42	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 318	2.87	171.56	H-Bond (Ligand Donor)	false
O2A	MG	MG- 1005	2.5	0	Metal Acceptor	false