Structure of PDB 6ms8 Chain D Binding Site BS01

Receptor Information

>6ms8 Chain D (length=207) Species: 3880 (Medicago truncatula)

VTALEIENYAFPPTVKPPGSTNNFFLGGAGERGIQIQDKFVKFTAIGVYL
QDIAVPYLAEKWKARSAHELTDTVPFFRDIVTGPFEKFMRVTMILPLTGH
QYSEKVSENCVAIWKSLGIYTDEEAKAIDKFVSVFKDETFPPGSSILFTV
SSLTISFSKDGSIPEVETAVIENKLLSQAVLESMIGAHGVSPAAKQSLAS
RLSKLFK

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: 6ms8 Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ms8 Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): R37 F48 T49 I51 Y107 V111 S193 V200
• Binding residue (residue number reindexed from 1): R32 F43 T44 I46 Y102 V106 S183 V190
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): R37 T49 M98 Y107
• Catalytic site (residue number reindexed from 1): R32 T44 M93 Y102
• Enzyme Commision number: 5.5.1.6: chalcone isomerase.

Gene Ontology

Molecular Function

• GO:0016853 isomerase activity
• GO:0016872 intramolecular lyase activity
• GO:0045430 chalcone isomerase activity

Biological Process

• GO:0009813 flavonoid biosynthetic process

External links

• PDB: RCSB:6ms8, PDBe:6ms8, PDBj:6ms8
• PDBsum: 6ms8
• UniProt: B7FJK3