Structure of PDB 3t96 Chain D Binding Site BS01

Receptor Information

>3t96 Chain D (length=258) Species: 10116 (Rattus norvegicus)

KTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKL
TIVGDGKYGCRDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFS
KPFMSLGISIMIKKGTPIESAEDLSKQTEIAYGTLDCGSTKEFFRRSKIA
VFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQR
KPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEQGLLDKLKNK
WWYDKGEC

Ligand information

• Ligand ID: IWD
• InChI: InChI=1S/C7H8IN3O4/c8-3-1-11(2-4(9)6(13)14)7(15)10-5(3)12/h1,4H,2,9H2,(H,13,14)(H,10,12,15)/t4-/m0/s1
• InChIKey: AXXYLTBQIQBTES-BYPYZUCNSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)C(N)CN1C=C(I)C(=O)NC1=O
  CACTVS 3.341: N[C@@H](CN1C=C(I)C(=O)NC1=O)C(O)=O
  OpenEye OEToolkits 1.5.0: C1=C(C(=O)NC(=O)N1CC(C(=O)O)N)I
  OpenEye OEToolkits 1.5.0: C1=C(C(=O)NC(=O)N1C[C@@H](C(=O)O)N)I
  CACTVS 3.341: N[CH](CN1C=C(I)C(=O)NC1=O)C(O)=O
• Formula: C7 H8 I N3 O4
• Name: 2-AMINO-3-(5-IODO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID;
  IODO-WILLARDIINE
• ChEMBL: CHEMBL121915
• DrugBank: DB02818
• ZINC: ZINC000002047688
• PDB chain: 3t96 Chain D Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3t96 Mechanism of AMPA Receptor Activation by Partial Agonists: DISULFIDE TRAPPING OF CLOSED LOBE CONFORMATIONS.
• Resolution: 1.872 Å
• Binding residue (original residue number in PDB): Y61 L90 T91 R96 L138 G141 S142 T143 L192 E193 M196
• Binding residue (residue number reindexed from 1): Y58 L87 T88 R93 L135 G138 S139 T140 L189 E190 M193
• Annotation score: 1
• Binding affinity: BindingDB: Ki=105nM

Gene Ontology

Molecular Function

• GO:0015276 ligand-gated monoatomic ion channel activity

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:3t96, PDBe:3t96, PDBj:3t96
• PDBsum: 3t96
• PubMed: 21846932
• UniProt: P19491|GRIA2_RAT Glutamate receptor 2 (Gene Name=Gria2)