Structure of PDB 3h52 Chain A Binding Site BS02

Receptor Information

>3h52 Chain A (length=247) Species: 9606 (Homo sapiens)

HMLTPTLVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAV
KWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAP
DLIINEQRMTLPDMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSV
PKDGLKSQALFDAIRMTYIKELGKAIVKREGNSSQNSQRFYQLTKLLDSM
HEVVENLLNYCFQTFLDKTMSIEFPEMLAEIITNQIPGNIKKLLFHQ

Ligand information

• Ligand ID: 486
• InChI: InChI=1S/C29H35NO2/c1-5-15-29(32)16-14-26-24-12-8-20-17-22(31)11-13-23(20)27(24)25(18-28(26,29)2)19-6-9-21(10-7-19)30(3)4/h6-7,9-10,17,24-26,32H,8,11-14,16,18H2,1-4H3/t24-,25+,26-,28-,29-/m0/s1
• InChIKey: VKHAHZOOUSRJNA-GCNJZUOMSA-N
• SMILES:
  ACDLabs 10.04: O=C5C=C4C(=C3C(c1ccc(N(C)C)cc1)CC2(C(CCC2(C#CC)O)C3CC4)C)CC5
  OpenEye OEToolkits 1.5.0: CC#CC1(CCC2C1(CC(C3=C4CCC(=O)C=C4CCC23)c5ccc(cc5)N(C)C)C)O
  CACTVS 3.341: CC#C[C]1(O)CC[CH]2[CH]3CCC4=CC(=O)CCC4=C3[CH](C[C]12C)c5ccc(cc5)N(C)C
  OpenEye OEToolkits 1.5.0: CC#C[C@@]1(CC[C@@H]2[C@@]1(C[C@@H](C3=C4CCC(=O)C=C4CC[C@@H]23)c5ccc(cc5)N(C)C)C)O
  CACTVS 3.341: CC#C[C@]1(O)CC[C@H]2[C@@H]3CCC4=CC(=O)CCC4=C3[C@H](C[C@]12C)c5ccc(cc5)N(C)C
• Formula: C29 H35 N O2
• Name: 11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE;
  RU-486;
  MIFEPRISTONE
• ChEMBL: CHEMBL1276308
• DrugBank: DB00834
• ZINC: ZINC000003831128
• PDB chain: 3h52 Chain A Residue 3

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3h52 Molecular switch in the glucocorticoid receptor: active and passive antagonist conformations
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): N564 G567 Q570 M601 F623 Q642 M752
• Binding residue (residue number reindexed from 1): N39 G42 Q45 M76 F98 Q117 M227
• Annotation score: 1
• Binding affinity: BindingDB: IC50=1.1nM,Ki=1.2nM,EC50=872nM,Kd=15nM

External links

• PDB: RCSB:3h52, PDBe:3h52, PDBj:3h52
• PDBsum: 3h52
• PubMed: 19913032
• UniProt: P04150|GCR_HUMAN Glucocorticoid receptor (Gene Name=NR3C1)