Structure of PDB 2kdh Chain A Binding Site BS02

Receptor Information

>2kdh Chain A (length=72) Species: 9606 (Homo sapiens)

MGKSEEELSDLFRMFDKNADGYIDLDELKIMLQATGETITEDDIEELMKD
GDKNNDGRIDYDEFLEFMKGVE

Ligand information

• Ligand ID: KDH
• InChI: InChI=1S/C22H18O11/c23-10-5-12(24)11-7-18(33-22(31)9-3-15(27)20(30)16(28)4-9)21(32-17(11)6-10)8-1-13(25)19(29)14(26)2-8/h1-6,18,21,23-30H,7H2/t18-,21-/m1/s1
• InChIKey: WMBWREPUVVBILR-WIYYLYMNSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1c(cc(c(c1O)O)O)[C@@H]2[C@@H](Cc3c(cc(cc3O2)O)O)OC(=O)c4cc(c(c(c4)O)O)O
  CACTVS 3.341: Oc1cc(O)c2C[C@@H](OC(=O)c3cc(O)c(O)c(O)c3)[C@H](Oc2c1)c4cc(O)c(O)c(O)c4
  OpenEye OEToolkits 1.5.0: c1c(cc(c(c1O)O)O)C2C(Cc3c(cc(cc3O2)O)O)OC(=O)c4cc(c(c(c4)O)O)O
  CACTVS 3.341: Oc1cc(O)c2C[CH](OC(=O)c3cc(O)c(O)c(O)c3)[CH](Oc2c1)c4cc(O)c(O)c(O)c4
  ACDLabs 10.04: O=C(OC2Cc3c(OC2c1cc(O)c(O)c(O)c1)cc(O)cc3O)c4cc(O)c(O)c(O)c4
• Formula: C22 H18 O11
• Name: (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate;
  (-)-Epigallocatechin-3-gallate;
  EGCG
• ChEMBL: CHEMBL297453
• DrugBank: DB12116
• ZINC: ZINC000003870412
• PDB chain: 2kdh Chain A Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2kdh Solution structure of human cardiac troponin C in complex with the green tea polyphenol, (-)-epigallocatechin 3-gallate
• Resolution: N/A
• Binding residue (original residue number in PDB): F104 L121 F156 M157 V160
• Binding residue (residue number reindexed from 1): F15 L32 F67 M68 V71
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=2.96,Kd=1.1mM

Gene Ontology

Molecular Function

• GO:0005509 calcium ion binding

External links

• PDB: RCSB:2kdh, PDBe:2kdh, PDBj:2kdh
• PDBsum: 2kdh
• PubMed: 19542563
• UniProt: P63316|TNNC1_HUMAN Troponin C, slow skeletal and cardiac muscles (Gene Name=TNNC1)