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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4ju2

2.700 Å

X-ray

2013-03-24

Interactomes:
Molecular Function:
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
B100 %


Ligand binding site composition:

B-Factor:78.759
Number of residues:32
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.673415.125

% Hydrophobic% Polar
60.1639.84
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4ju2HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802550Highcharts.com
Ligand :
4ju2_2 Structure
HET Code: 1O0
Formula: C27H15F6N3O2
Molecular weight: 527.417 g/mol
DrugBank ID: -
Buried Surface Area:64.24 %
Polar Surface area: 54.79 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 0
Rings: 5
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-22.9494-21.7732-17.6106
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4ju2RingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


Binding mode :
What is Poseview ?
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C16CD1LEU- 4193.880Hydrophobic
F29CD2LEU- 4193.220Hydrophobic
C14CD2LEU- 4193.620Hydrophobic
C3CD1LEU- 4193.730Hydrophobic
C3CBARG- 4224.260Hydrophobic
F28CGARG- 4224.330Hydrophobic
F19CEMET- 4233.480Hydrophobic
C34CEMET- 4233.690Hydrophobic
F28CBMET- 4233.470Hydrophobic
F31CBHIS- 4754.370Hydrophobic
N8NSER- 4762.73142.98H-Bond
(Protein Donor)
O18NTYR- 4773.08152.98H-Bond
(Protein Donor)
F31CE1TYR- 4773.590Hydrophobic
C13CD1ILE- 4823.940Hydrophobic
C14CG2ILE- 4824.080Hydrophobic
C21CG2ILE- 4824.050Hydrophobic
F29CG2ILE- 4823.640Hydrophobic
F29CBVAL- 4853.850Hydrophobic
F30CG1VAL- 4853.540Hydrophobic
F30CBALA- 4863.710Hydrophobic
C37CBLEU- 4893.490Hydrophobic
F30CD1LEU- 4893.420Hydrophobic
C38CD1LEU- 4893.490Hydrophobic
C15CD2LEU- 4974.280Hydrophobic
C23CD2LEU- 4974.220Hydrophobic
C24CBLEU- 4974.210Hydrophobic
F32CD1LEU- 4974.160Hydrophobic
C34CBLEU- 4974.170Hydrophobic
F28CE2TRP- 5283.430Hydrophobic
F32CE3TRP- 5284.090Hydrophobic