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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:

3kgc

1.550 Å

X-ray

2009-10-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glutamate receptor 2
ID:GRIA2_RAT
AC:P19491
Organism:Rattus norvegicus
Reign:Eukaryota
TaxID:10116
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A54 %
B46 %


Ligand binding site composition:

B-Factor:11.932
Number of residues:37
Including
Standard Amino Acids: 37
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0991596.375

% Hydrophobic% Polar
47.1552.85
According to VolSite

Ligand :
3kgc_1 Structure
HET Code: LY7
Formula: C19H22N2O2S
Molecular weight: 342.455 g/mol
DrugBank ID: -
Buried Surface Area:71.28 %
Polar Surface area: 78.34 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
16.076647.2499-2.27283


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
CABCG2ILE- 923.930Hydrophobic
CAACBLYS- 1044.080Hydrophobic
CAJCGPRO- 1054.160Hydrophobic
CALCGPRO- 1053.910Hydrophobic
CAKCBPRO- 1053.950Hydrophobic
CAMCGPRO- 1053.470Hydrophobic
NAQOPRO- 1052.8149.75H-Bond
(Ligand Donor)
CAKCBSER- 1084.150Hydrophobic
CAOCBSER- 1083.760Hydrophobic
CACCBSER- 2174.340Hydrophobic
CARCBSER- 2173.970Hydrophobic
CABCBLYS- 2184.290Hydrophobic
CAACG1VAL- 2384.210Hydrophobic
CABCD2LEU- 2393.660Hydrophobic
NADOGSER- 2423.06161.05H-Bond
(Protein Donor)
CAACBSER- 2423.670Hydrophobic