Structure of PDB 5awj Chain A Binding Site BS02

Receptor Information
>5awj Chain A (length=240) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMSPLSMLPHLADLV
SYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDM
SWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLM
AICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMI
QKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN
Ligand information
Ligand IDYSL
InChIInChI=1S/C30H50O3/c1-5-6-7-8-10-24(16-18-31)21(2)26-14-15-27-25(11-9-17-30(26,27)4)13-12-23-19-28(32)22(3)29(33)20-23/h12-13,21,24,26-29,31-33H,3,5-11,14-20H2,1-2,4H3/b25-13+/t21-,24+,26-,27+,28-,29-,30-/m1/s1
InChIKeyJUQILRKVRIIJNO-FJOOTJEJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CCCCCC[C@@H](CCO)[C@@H](C)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C
CACTVS 3.385CCCCCC[C@@H](CCO)[C@@H](C)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3/C[C@@H](O)C(=C)[C@H](O)C3
OpenEye OEToolkits 1.9.2CCCCCCC(CCO)C(C)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
CACTVS 3.385CCCCCC[CH](CCO)[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
FormulaC30 H50 O3
Name(1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-(2-hydroxyethyl)nonan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol
ChEMBLCHEMBL3629552
DrugBank
ZINCZINC000263620625
PDB chain5awj Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5awj Fine tuning of agonistic/antagonistic activity for vitamin D receptor by 22-alkyl chain length of ligands: 22S-Hexyl compound unexpectedly restored agonistic activity.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		Y143 S233 R270 S271 S274 W282 C284 H393
Binding residue
(residue number reindexed from 1)		Y21 S53 R90 S91 S94 W102 C104 H213
Annotation score1
Binding affinityMOAD: ic50=0.21nM
PDBbind-CN: -logKd/Ki=9.68,IC50=0.21nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004879 nuclear receptor activity
Biological Process
GO:0006355 regulation of DNA-templated transcription

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5awj, PDBe:5awj, PDBj:5awj
PDBsum5awj
PubMed26515040
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

[Back to BioLiP]