Structure of PDB 3w0h Chain A Binding Site BS02

Receptor Information

>3w0h Chain A (length=247) Species: 10116 (Rattus norvegicus)

SHDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMSPLSML
PHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQ
SFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHE
EEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSH
QLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN

Ligand information

• Ligand ID: W12
• InChI: InChI=1S/C28H42O5/c1-6-16-28(17-7-2,21-8-12-24(13-9-21)32-19-23(30)18-29)22-10-14-25(15-11-22)33-20-26(31)27(3,4)5/h8-15,23,26,29-31H,6-7,16-20H2,1-5H3/t23-,26-/m0/s1
• InChIKey: PJASVJJQJUYPCG-OZXSUGGESA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: CCCC(CCC)(c1ccc(cc1)OC[C@H](CO)O)c2ccc(cc2)OC[C@@H](C(C)(C)C)O
  CACTVS 3.370: CCCC(CCC)(c1ccc(OC[C@@H](O)CO)cc1)c2ccc(OC[C@H](O)C(C)(C)C)cc2
  ACDLabs 12.01: O(c1ccc(cc1)C(c2ccc(OCC(O)C(C)(C)C)cc2)(CCC)CCC)CC(O)CO
  OpenEye OEToolkits 1.7.6: CCCC(CCC)(c1ccc(cc1)OCC(CO)O)c2ccc(cc2)OCC(C(C)(C)C)O
  CACTVS 3.370: CCCC(CCC)(c1ccc(OC[CH](O)CO)cc1)c2ccc(OC[CH](O)C(C)(C)C)cc2
• Formula: C28 H42 O5
• Name: (2S)-3-{4-[4-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}phenyl)heptan-4-yl]phenoxy}propane-1,2-diol
• ZINC: ZINC000095921206
• PDB chain: 3w0h Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3w0h Structural basis for vitamin D receptor agonism by novel non-secosteroidal ligands.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): Y143 L226 A227 L229 I267 M268 S271 S274 W282 H301 H393
• Binding residue (residue number reindexed from 1): Y28 L53 A54 L56 I94 M95 S98 S101 W109 H128 H220
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0004879 nuclear receptor activity

Biological Process

• GO:0006355 regulation of DNA-templated transcription

External links

• PDB: RCSB:3w0h, PDBe:3w0h, PDBj:3w0h
• PDBsum: 3w0h
• PubMed: 23462137
• UniProt: P13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)