Structure of PDB 4nwd Chain A Binding Site BS01

Receptor Information

>4nwd Chain A (length=254) Species: 10116 (Rattus norvegicus)

NRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYE
IRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFS
KPFMTLGVSILYRKGTPIDSADDLAKQTKIEYGAVKDGATMTFFKKSKIS
TFEKMWAFMSSKPSALVKNNEEGIQRTLTADYALLMESTTIEYITQRNCN
LTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRG
SGCP

Ligand information

• Ligand ID: 2QD
• InChI: InChI=1S/C9H16N2O5/c1-11-7(12)3-2-5(8(13)14)4-6(10)9(15)16/h5-6H,2-4,10H2,1H3,(H,11,12)(H,13,14)(H,15,16)/t5-,6+/m1/s1
• InChIKey: NIJAFEMYFNBSBE-RITPCOANSA-N
• SMILES:
  ACDLabs 12.01: O=C(O)C(N)CC(C(=O)O)CCC(=O)NC
  OpenEye OEToolkits 1.7.6: CNC(=O)CC[C@H](C[C@@H](C(=O)O)N)C(=O)O
  CACTVS 3.385: CNC(=O)CC[C@H](C[C@H](N)C(O)=O)C(O)=O
  CACTVS 3.385: CNC(=O)CC[CH](C[CH](N)C(O)=O)C(O)=O
  OpenEye OEToolkits 1.7.6: CNC(=O)CCC(CC(C(=O)O)N)C(=O)O
• Formula: C9 H16 N2 O5
• Name: (4R)-4-[3-(methylamino)-3-oxopropyl]-L-glutamic acid
• ChEMBL: CHEMBL500042
• ZINC: ZINC000040974521
• PDB chain: 4nwd Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4nwd Molecular Recognition of Two 2,4-syn-Functionalized (S)-Glutamate Analogues by the Kainate Receptor GluK3 Ligand Binding Domain.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): E15 Y63 P90 L91 T92 R97 G142 A143 T144 N174 E191 Y217
• Binding residue (residue number reindexed from 1): E11 Y59 P86 L87 T88 R93 G138 A139 T140 N170 E187 Y213
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.40,Ki=3.96uM
  BindingDB: Ki=57.3nM

Gene Ontology

Molecular Function

• GO:0015276 ligand-gated monoatomic ion channel activity

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:4nwd, PDBe:4nwd, PDBj:4nwd
• PDBsum: 4nwd
• PubMed: 25044437
• UniProt: P42264|GRIK3_RAT Glutamate receptor ionotropic, kainate 3 (Gene Name=Grik3)