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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:

3ijo

2.000 Å

X-ray

2009-08-04

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
B36 %
E64 %


Ligand binding site composition:

B-Factor:28.013
Number of residues:35
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.3681147.500

% Hydrophobic% Polar
45.8854.12
According to VolSite

Ligand :
3ijo_2 Structure
HET Code: B4D
Formula: C11H14ClN3O4S3
Molecular weight: 383.895 g/mol
DrugBank ID: -
Buried Surface Area:63.17 %
Polar Surface area: 160.41 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 3
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-5.0736452.1325-20.9215


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
C03CBILE- 923.210Hydrophobic
C03CGLYS- 1044.230Hydrophobic
S04CBLYS- 1044.480Hydrophobic
S04CGPRO- 1054.430Hydrophobic
N22OPRO- 1052.94174.62H-Bond
(Ligand Donor)
O15NSER- 1083.33173.73H-Bond
(Protein Donor)
N14OGSER- 2173.44123.88H-Bond
(Ligand Donor)
C12CBSER- 2173.970Hydrophobic
C05CBLYS- 2184.420Hydrophobic
C03CD2LEU- 2393.840Hydrophobic
C05CBSER- 2424.290Hydrophobic
N07OGSER- 2422.84128.13H-Bond
(Ligand Donor)
C09CD1LEU- 2473.750Hydrophobic
CL11CBLEU- 2473.580Hydrophobic
CL11CBASP- 2483.80Hydrophobic