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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:

4awm

2.600 Å

X-ray

2012-06-04

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:36.898
Number of residues:32
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
0.421718.875

% Hydrophobic% Polar
41.3158.69
According to VolSite

Ligand :
4awm_1 Structure
HET Code: KDH
Formula: C22H18O11
Molecular weight: 458.372 g/mol
DrugBank ID: DB12116
Buried Surface Area:53.65 %
Polar Surface area: 197.36 Å2
Number of
H-Bond Acceptors: 11
H-Bond Donors: 8
Rings: 4
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 4

Mass center Coordinates

XYZ
9.80676-33.8119.8652


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
C01CE2TYR- 244.140Hydrophobic
C26CBTYR- 243.840Hydrophobic
DuArDuArTYR- 243.830Aromatic Face/Face
O03OE1GLU- 263.12152.32H-Bond
(Ligand Donor)
C43CBALA- 373.640Hydrophobic
C01CD1ILE- 384.370Hydrophobic
C41CG1ILE- 383.550Hydrophobic
C39CBHIS- 413.680Hydrophobic
O50OVAL- 1223.04147.48H-Bond
(Ligand Donor)
O10NZLYS- 1342.99157.65H-Bond
(Protein Donor)
O1MN MN- 9012.220Metal Acceptor
O7MN MN- 9012.140Metal Acceptor
DuArMN MN- 9013.9796.25Pi/Cation
O1MN MN- 9021.930Metal Acceptor