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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:

4e5l

2.470 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
C100 %


Ligand binding site composition:

B-Factor:44.223
Number of residues:19
Including
Standard Amino Acids: 16
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.6691110.375

% Hydrophobic% Polar
34.3565.65
According to VolSite

Ligand :
4e5l_3 Structure
HET Code: DBH
Formula: C7H5O4
Molecular weight: 153.112 g/mol
DrugBank ID: DB01672
Buried Surface Area:34.76 %
Polar Surface area: 80.59 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 1
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-6.15418-16.163119.073


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
O6NZLYS- 1343.15134.26H-Bond
(Protein Donor)
O3MN MN- 3012.480Metal Acceptor
O6MN MN- 3012.540Metal Acceptor
O9MN MN- 3022.130Metal Acceptor
O3MN MN- 3022.130Metal Acceptor
O6OHOH- 4013.02139.1H-Bond
(Ligand Donor)