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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:

4isu

2.300 Å

X-ray

2013-01-17

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
B100 %


Ligand binding site composition:

B-Factor:18.154
Number of residues:25
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: CL

Cavity properties

LigandabilityVolume (Å3)
0.330641.250

% Hydrophobic% Polar
40.5359.47
According to VolSite

Ligand :
4isu_2 Structure
HET Code: IKM
Formula: C12H13N2O6
Molecular weight: 281.241 g/mol
DrugBank ID: -
Buried Surface Area:59.59 %
Polar Surface area: 135.19 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 2
Rings: 3
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-23.648862.040849.9375


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
C5CE2TYR- 613.80Hydrophobic
N2OPRO- 893.12141.83H-Bond
(Ligand Donor)
O6NTHR- 912.93163.96H-Bond
(Protein Donor)
O6OG1THR- 912.89148.26H-Bond
(Protein Donor)
O3NH2ARG- 962.72134.46H-Bond
(Protein Donor)
O6NH1ARG- 962.96141.56H-Bond
(Protein Donor)
O3CZARG- 963.590Ionic
(Protein Cationic)
O6CZARG- 963.650Ionic
(Protein Cationic)
O4NSER- 1422.66141.83H-Bond
(Protein Donor)
C8CGGLU- 1934.340Hydrophobic
N1OE1GLU- 1933161.89H-Bond
(Ligand Donor)
N1OE2GLU- 1932.72131.6H-Bond
(Ligand Donor)
N1OE1GLU- 19330Ionic
(Ligand Cationic)
N1OE2GLU- 1932.720Ionic
(Ligand Cationic)