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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:

4e5h

2.160 Å

X-ray

2012-03-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Polymerase acidic protein
ID:Q5EP34_9INFA
AC:Q5EP34
Organism:Influenza A virus )
Reign:Viruses
TaxID:284218
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:48.480
Number of residues:27
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.067691.875

% Hydrophobic% Polar
33.1766.83
According to VolSite

Ligand :
4e5h_1 Structure
HET Code: 0N8
Formula: C23H24ClNO4
Molecular weight: 413.894 g/mol
DrugBank ID: -
Buried Surface Area:50.95 %
Polar Surface area: 81.87 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
-51.9851-15.054124.9215


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
C20CE1TYR- 243.320Hydrophobic
CL2CDLYS- 344.240Hydrophobic
CL2CD1ILE- 383.620Hydrophobic
C6CZ2TRP- 883.370Hydrophobic
C13CBPHE- 1054.040Hydrophobic
C6CBPHE- 1053.680Hydrophobic
C12CBLEU- 1063.990Hydrophobic
C1CBLEU- 1063.680Hydrophobic
O25NZLYS- 1343.46126.47H-Bond
(Protein Donor)
O25NZLYS- 1343.460Ionic
(Protein Cationic)
O28MN MN- 3032.350Metal Acceptor
O25MN MN- 3031.940Metal Acceptor
O27MN MN- 3041.930Metal Acceptor
O28MN MN- 3042.340Metal Acceptor
O25OHOH- 4012.98163.56H-Bond
(Protein Donor)