Structure of PDB 1yim Chain A Binding Site BS01

Receptor Information

>1yim Chain A (length=245) Species: 9606 (Homo sapiens)

ALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVH
MINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAP
NLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNS
GVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQ
LLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHA

Ligand information

• Ligand ID: CM4
• InChI: InChI=1S/C28H31NO4/c1-19-25-18-23(31)10-13-26(25)33-28(27(19)20-4-8-22(30)9-5-20)21-6-11-24(12-7-21)32-17-16-29-14-2-3-15-29/h4-13,18-19,27-28,30-31H,2-3,14-17H2,1H3/t19-,27-,28+/m1/s1
• InChIKey: XPVKGTWRXBSJKO-LHXLBICKSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C[C@@H]1c2cc(ccc2O[C@H]([C@H]1c3ccc(cc3)O)c4ccc(cc4)OCCN5CCCC5)O
  OpenEye OEToolkits 1.5.0: CC1c2cc(ccc2OC(C1c3ccc(cc3)O)c4ccc(cc4)OCCN5CCCC5)O
  CACTVS 3.341: C[C@H]1[C@@H]([C@@H](Oc2ccc(O)cc12)c3ccc(OCCN4CCCC4)cc3)c5ccc(O)cc5
  CACTVS 3.341: C[CH]1[CH]([CH](Oc2ccc(O)cc12)c3ccc(OCCN4CCCC4)cc3)c5ccc(O)cc5
  ACDLabs 10.04: Oc1ccc(cc1)C4C(c5c(OC4c3ccc(OCCN2CCCC2)cc3)ccc(O)c5)C
• Formula: C28 H31 N O4
• Name: (2R,3R,4S)-3-(4-HYDROXYPHENYL)-4-METHYL-2-[4-(2-PYRROLIDIN-1-YLETHOXY)PHENYL]CHROMAN-6-OL
• ChEMBL: CHEMBL181936
• DrugBank: DB07567
• ZINC: ZINC000016051697
• PDB chain: 1yim Chain A Residue 600

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1yim Estrogen receptor ligands. Part 10: Chromanes: old scaffolds for new SERAMs.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): L346 T347 A350 D351 E353 W383 L387 F404 M421 G521 H524 L525 K531
• Binding residue (residue number reindexed from 1): L40 T41 A44 D45 E47 W77 L81 F98 M115 G215 H218 L219 K225
• Annotation score: 1
• Binding affinity: MOAD: ic50=1.5nM
  BindingDB: IC50=1.5nM

External links

• PDB: RCSB:1yim, PDBe:1yim, PDBj:1yim
• PDBsum: 1yim
• PubMed: 15745820
• UniProt: P03372|ESR1_HUMAN Estrogen receptor (Gene Name=ESR1)