Structure of PDB 4mdd Chain B Binding Site BS02

Receptor Information

>4mdd Chain B (length=220) Species: 9606 (Homo sapiens)

TLVSALETIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKA
IPGFRNLHLDDQMTLLQYSWMYLMAFALGWRSYRQSSANLLCFAPDLIIN
EQRMTLPDMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGL
KSQALFDAIRMTYIKELGKAIVKREGNSSQNSQRFYQLTKLLDSMHEVVE
NLLNYCFQTFLNIKKLLFHQ

Ligand information

• Ligand ID: 29M
• InChI: InChI=1S/C28H32FN3O3S/c1-18(2)20-13-23-27(22-12-11-21(29)15-26(22)35-4)25(17-32(3)16-19-9-7-6-8-10-19)30-28(23)24(14-20)31-36(5,33)34/h6-15,18,30-31H,16-17H2,1-5H3
• InChIKey: MFAGIEMFDDDLMT-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: COc1cc(F)ccc1c2c(CN(C)Cc3ccccc3)[nH]c4c(N[S](C)(=O)=O)cc(cc24)C(C)C
  OpenEye OEToolkits 1.7.6: CC(C)c1cc2c(c([nH]c2c(c1)NS(=O)(=O)C)CN(C)Cc3ccccc3)c4ccc(cc4OC)F
  ACDLabs 12.01: O=S(=O)(Nc1cc(cc2c1nc(c2c3ccc(F)cc3OC)CN(Cc4ccccc4)C)C(C)C)C
• Formula: C28 H32 F N3 O3 S
• Name: N-[2-{[benzyl(methyl)amino]methyl}-3-(4-fluoro-2-methoxyphenyl)-5-(propan-2-yl)-1H-indol-7-yl]methanesulfonamide
• ChEMBL: CHEMBL3605919
• ZINC: ZINC000219221856
• PDB chain: 4mdd Chain B Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4mdd Crystal Structure of the Glucocorticoid Receptor Bound to a Non-steroidal Antagonist Reveals Repositioning and Partial Disordering of Activation Function Helix 12
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): M560 L563 N564 G567 Q570 M601 M604 A605 L608 F623 M646 Y735 C736 F737
• Binding residue (residue number reindexed from 1): M30 L33 N34 G37 Q40 M71 M74 A75 L78 F93 M116 Y205 C206 F207
• Annotation score: 1
• Binding affinity: BindingDB: Ki=1.2nM,IC50=2.8nM

External links

• PDB: RCSB:4mdd, PDBe:4mdd, PDBj:4mdd
• PDBsum: 4mdd
• UniProt: P04150|GCR_HUMAN Glucocorticoid receptor (Gene Name=NR3C1)