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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:

2d3u

2.000 Å

X-ray

2005-10-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Polyprotein
ID:Q99AU2_9HEPC
AC:Q99AU2
Organism:Hepatitis C virus subtype 1b
Reign:Viruses
TaxID:31647
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:25.543
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.629371.250

% Hydrophobic% Polar
59.0940.91
According to VolSite

Ligand :
2d3u_2 Structure
HET Code: CCT
Formula: C19H13N2O4S2
Molecular weight: 397.448 g/mol
DrugBank ID: DB07547
Buried Surface Area:59.54 %
Polar Surface area: 146.71 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-9.3169632.6825-29.6856


Binding mode :
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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
C6CD1LEU- 4193.950Hydrophobic
S11CD2LEU- 4193.80Hydrophobic
C5CD2LEU- 4193.670Hydrophobic
C22CD1LEU- 4193.790Hydrophobic
C23CBARG- 4223.990Hydrophobic
C1SDMET- 4233.610Hydrophobic
C22CBMET- 4233.580Hydrophobic
C25CBHIS- 4753.970Hydrophobic
O16NSER- 4762.68151.63H-Bond
(Protein Donor)
O15NTYR- 4772.69156.13H-Bond
(Protein Donor)
C25CE1TYR- 4774.060Hydrophobic
S11CD1ILE- 4823.650Hydrophobic
C4CG2ILE- 4823.730Hydrophobic
C21CD1LEU- 4973.920Hydrophobic
C1CBLEU- 4974.080Hydrophobic
C22CE3TRP- 5283.310Hydrophobic
C19CBTRP- 5283.780Hydrophobic