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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:

5d9j

1.850 Å

X-ray

2015-08-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Polymerase acidic protein
ID:C3W5S0_I09A0
AC:C3W5S0
Organism:Influenza A virus
Reign:Viruses
TaxID:641501
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:35.261
Number of residues:27
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 2
Water Molecules: 4
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.506583.875

% Hydrophobic% Polar
44.5155.49
According to VolSite

Ligand :
5d9j_1 Structure
HET Code: 0N8
Formula: C23H24ClNO4
Molecular weight: 413.894 g/mol
DrugBank ID: -
Buried Surface Area:39.82 %
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
84.395787.86167.86064


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
CL2CBALA- 373.80Hydrophobic
C20CG1ILE- 384.380Hydrophobic
CL2CG1ILE- 383.860Hydrophobic
C20CBHIS- 414.470Hydrophobic
O26NZLYS- 1153.270Ionic
(Protein Cationic)
O25NZLYS- 1153.20Ionic
(Protein Cationic)
O25NZLYS- 1153.2131.17H-Bond
(Protein Donor)
O28MN MN- 2012.180Metal Acceptor
O25MN MN- 2011.910Metal Acceptor
O27MN MN- 2022.040Metal Acceptor
O28MN MN- 2022.130Metal Acceptor
O25OHOH- 3293179.98H-Bond
(Protein Donor)
O28OHOH- 3332.82136.85H-Bond
(Ligand Donor)