Structure of PDB 3g8o Chain A Binding Site BS01

Receptor Information

>3g8o Chain A (length=250) Species: 9606 (Homo sapiens)

QLIPPLINLLMSIEPDVIYAGHDNTKDTSSSLLTSLNQLGERQLLSVVKW
SKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDL
ILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPL
EGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHD
LVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMVKPLLFHK

Ligand information

• Ligand ID: 30X
• InChI: InChI=1S/C15H15F6N3O/c1-9(13(25)23(2)3)24(8-14(16,17)18)11-5-4-10(7-22)12(6-11)15(19,20)21/h4-6,9H,8H2,1-3H3/t9-/m0/s1
• InChIKey: BEFAEFLFXOZVJY-VIFPVBQESA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C(=O)N(C)C)N(CC(F)(F)F)c1ccc(c(c1)C(F)(F)F)C#N
  CACTVS 3.341: C[C@H](N(CC(F)(F)F)c1ccc(C#N)c(c1)C(F)(F)F)C(=O)N(C)C
  ACDLabs 10.04: O=C(N(C)C)C(N(c1cc(c(C#N)cc1)C(F)(F)F)CC(F)(F)F)C
  OpenEye OEToolkits 1.5.0: C[C@@H](C(=O)N(C)C)[N@@](CC(F)(F)F)c1ccc(c(c1)C(F)(F)F)C#N
  CACTVS 3.341: C[CH](N(CC(F)(F)F)c1ccc(C#N)c(c1)C(F)(F)F)C(=O)N(C)C
• Formula: C15 H15 F6 N3 O
• Name: N~2~-[4-cyano-3-(trifluoromethyl)phenyl]-N,N-dimethyl-N~2~-(2,2,2-trifluoroethyl)-L-alaninamide
• ZINC: ZINC000043020005
• PDB chain: 3g8o Chain A Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3g8o Rational design of orally-active, pyrrolidine-based progesterone receptor partial agonists.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): L718 N719 L721 M756 M759 V760 L763 L797 L887 Y890 C891 T894
• Binding residue (residue number reindexed from 1): L36 N37 L39 M74 M77 V78 L81 L115 L205 Y208 C209 T212
• Annotation score: 1
• Binding affinity: MOAD: ic50=125nM
  PDBbind-CN: -logKd/Ki=7.80,IC50=16nM
  BindingDB: IC50=125nM,EC50=1300nM

External links

• PDB: RCSB:3g8o, PDBe:3g8o, PDBj:3g8o
• PDBsum: 3g8o
• PubMed: 19595590
• UniProt: P06401|PRGR_HUMAN Progesterone receptor (Gene Name=PGR)