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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:

5fdg

2.100 Å

X-ray

2015-12-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Polymerase acidic protein
ID:PA_I34A1
AC:P03433
Organism:Influenza A virus
Reign:Viruses
TaxID:211044
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:34.522
Number of residues:28
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.598627.750

% Hydrophobic% Polar
41.4058.60
According to VolSite

Ligand :
5fdg_1 Structure
HET Code: 0N8
Formula: C23H24ClNO4
Molecular weight: 413.894 g/mol
DrugBank ID: -
Buried Surface Area:50.32 %
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
1.2470433.068815.9724


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
C4CG1ILE- 434.180Hydrophobic
C5CBHIS- 464.070Hydrophobic
C16CBPHE- 904.190Hydrophobic
C15CBLEU- 914.340Hydrophobic
C18CGGLU- 1044.40Hydrophobic
CL2CDLYS- 1193.690Hydrophobic
O26NZLYS- 1192.9159.57H-Bond
(Protein Donor)
O26NZLYS- 1192.90Ionic
(Protein Cationic)
CL2CBLYS- 1223.960Hydrophobic
C20CDLYS- 1224.260Hydrophobic
CL2CG2ILE- 1234.180Hydrophobic
O28MN MN- 2022.440Metal Acceptor
O25MN MN- 2022.230Metal Acceptor
O27MN MN- 2032.250Metal Acceptor
O28MN MN- 2032.130Metal Acceptor
O26OHOH- 3083.48127.05H-Bond
(Protein Donor)