Structure of PDB 4d06 Chain A Binding Site BS01

Receptor Information

>4d06 Chain A (length=282) Species: 39490 (Eubacterium ramulus)

ADFKFEPMRSLIYVDCVSEDYRPKLQRWIYKVHIPDSISQFEPYVTKYAF
YPSFPIPPQGDRFGYARMQLTEHHWLVSDLDPRLEIKAIAETFPMDVLVW
QGQIPAAAHTDAQIDSDGDAGNAARKSNNAEGNPFIFAFLPMWWEKDLKG
KGRTIEDGANYRFNMTIGFPEGVDKAEGEKWLFEKVVPILQAAPECTRVL
ASAVKKDINGCVMDWVLEIWFENQSGWYKVMVDDMKALEKPSWAQQDAFP
FLKPYHNVCSAAVADYTPSNNLANYRGYITMR

Ligand information

• Ligand ID: NAR
• InChI: InChI=1S/C15H12O5/c16-9-3-1-8(2-4-9)13-7-12(19)15-11(18)5-10(17)6-14(15)20-13/h1-6,13,16-18H,7H2/t13-/m0/s1
• InChIKey: FTVWIRXFELQLPI-ZDUSSCGKSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1cc(ccc1C2CC(=O)c3c(cc(cc3O2)O)O)O
  CACTVS 3.341: Oc1ccc(cc1)[CH]2CC(=O)c3c(O)cc(O)cc3O2
  OpenEye OEToolkits 1.5.0: c1cc(ccc1[C@@H]2CC(=O)c3c(cc(cc3O2)O)O)O
  ACDLabs 10.04: O=C2c3c(OC(c1ccc(O)cc1)C2)cc(O)cc3O
  CACTVS 3.341: Oc1ccc(cc1)[C@@H]2CC(=O)c3c(O)cc(O)cc3O2
• Formula: C15 H12 O5
• Name: NARINGENIN
• ChEMBL: CHEMBL9352
• DrugBank: DB03467
• ZINC: ZINC000000156701
• PDB chain: 4d06 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4d06 Structure and Catalytic Mechanism of the Evolutionarily Unique Bacterial Chalcone Isomerase
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): H33 Y48 F50 T71 H73 D79 Q101 R125 F135
• Binding residue (residue number reindexed from 1): H33 Y48 F50 T71 H73 D79 Q101 R125 F135
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 5.5.1.6: chalcone isomerase.

Gene Ontology

Molecular Function

• GO:0016853 isomerase activity
• GO:0045430 chalcone isomerase activity

External links

• PDB: RCSB:4d06, PDBe:4d06, PDBj:4d06
• PDBsum: 4d06
• PubMed: 25849401
• UniProt: V9P0A9