Structure of PDB 6k5o Chain A Binding Site BS02

Receptor Information

>6k5o Chain A (length=237) Species: 10116 (Rattus norvegicus)

KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRPLSMLPHLADLVSY
SIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSW
DCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAI
CIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQK
LADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFG

Ligand information

• Ligand ID: D0O
• InChI: InChI=1S/C25H42O5S/c1-16(5-10-23(26)27)20-8-9-21-19-7-6-17-15-18(30-31(4,28)29)11-13-24(17,2)22(19)12-14-25(20,21)3/h16-22H,5-15H2,1-4H3,(H,26,27)/t16-,17-,18-,19+,20-,21+,22+,24+,25-/m1/s1
• InChIKey: QKDRPUDDQCLYDP-ULCLHEGSSA-N
• SMILES:
  CACTVS 3.385: C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@@H](CC[C@]4(C)[C@H]3CC[C@]12C)O[S](C)(=O)=O
  CACTVS 3.385: C[CH](CCC(O)=O)[CH]1CC[CH]2[CH]3CC[CH]4C[CH](CC[C]4(C)[CH]3CC[C]12C)O[S](C)(=O)=O
  OpenEye OEToolkits 2.0.7: C[C@H](CCC(=O)O)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC[C@H]4[C@@]3(CC[C@H](C4)OS(=O)(=O)C)C)C
  OpenEye OEToolkits 2.0.7: CC(CCC(=O)O)C1CCC2C1(CCC3C2CCC4C3(CCC(C4)OS(=O)(=O)C)C)C
• Formula: C25 H42 O5 S
• Name: (4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3-methylsulfonyloxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoic acid
• ChEMBL: CHEMBL4540985
• PDB chain: 6k5o Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6k5o Development of novel lithocholic acid derivatives as vitamin D receptor agonists.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): Y143 S271 S274 W282
• Binding residue (residue number reindexed from 1): Y21 S89 S92 W100
• 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:6k5o, PDBe:6k5o, PDBj:6k5o
• PDBsum: 6k5o
• PubMed: 31300316
• UniProt: P13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)