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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:

5cgv

2.170 Å

X-ray

2015-07-09

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:34.508
Number of residues:30
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 2
Water Molecules: 3
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.333533.250

% Hydrophobic% Polar
44.9455.06
According to VolSite

Ligand :
5cgv_1 Structure
HET Code: 0N8
Formula: C23H24ClNO4
Molecular weight: 413.894 g/mol
DrugBank ID: -
Buried Surface Area:49.35 %
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
-28.0413-17.102917.5473


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
C2CBALA- 204.230Hydrophobic
C4CD1TYR- 243.450Hydrophobic
C1CG1ILE- 384.290Hydrophobic
C6CD1ILE- 383.470Hydrophobic
O28NE2HIS- 413.21139.92H-Bond
(Ligand Donor)
C17CBPHE- 1054.180Hydrophobic
C16CBPHE- 1054.030Hydrophobic
C18CGGLU- 1194.480Hydrophobic
CL2CGLYS- 1343.840Hydrophobic
O26NZLYS- 1343.520Ionic
(Protein Cationic)
O25NZLYS- 1342.920Ionic
(Protein Cationic)
O25NZLYS- 1342.92129.39H-Bond
(Protein Donor)
CL2CBLYS- 1373.560Hydrophobic
C18CD1ILE- 13840Hydrophobic
CL2CD1ILE- 1383.80Hydrophobic
O28MN MN- 3012.340Metal Acceptor
O26MN MN- 3012.320Metal Acceptor
O27MN MN- 3022.230Metal Acceptor
O28MN MN- 3022.070Metal Acceptor