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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:

3rn8

1.700 Å

X-ray

2011-04-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glutamate receptor 2
ID:GRIA2_HUMAN
AC:P42262
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A50 %
C50 %


Ligand binding site composition:

B-Factor:18.055
Number of residues:39
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.842425.250

% Hydrophobic% Polar
36.5163.49
According to VolSite

Ligand :
3rn8_1 Structure
HET Code: RN8
Formula: C22H14N2O4S2
Molecular weight: 434.488 g/mol
DrugBank ID: -
Buried Surface Area:65.74 %
Polar Surface area: 184.32 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 0
Rings: 3
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
61.105926.208843.1824


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
C5CGPRO- 1053.370Hydrophobic
C4CGPRO- 1053.310Hydrophobic
O28OGSER- 1082.91135.42H-Bond
(Protein Donor)
O27OGSER- 1082.79140.57H-Bond
(Protein Donor)
C4CBSER- 1083.730Hydrophobic
C5CBSER- 1083.710Hydrophobic
S30CBSER- 2174.460Hydrophobic
C2CG1VAL- 2384.060Hydrophobic
C1CG1VAL- 2383.910Hydrophobic
C1CD2LEU- 2393.920Hydrophobic
C2CD2LEU- 2393.940Hydrophobic
C1CBASN- 2423.750Hydrophobic
C2CBASN- 2423.720Hydrophobic