Structure of PDB 5ien Chain A Binding Site BS01

Receptor Information

>5ien Chain A (length=129) Species: 32630 (synthetic construct)

QSAKEAIEAALADFVKAYNSKDAAGVASKYMDDAAIFPLDMARVDGRQNI
QKLWQGLMDMGVSEPKLTTLDVQESGDFAFESGSISLKGPGKDSKLVDIA
GKYVEVWRKGQDGGWKLYRTIANLDPAEH

Ligand information

• Ligand ID: VDY
• InChI: InChI=1S/C27H44O2/c1-19-10-13-23(28)18-22(19)12-11-21-9-7-17-27(5)24(14-15-25(21)27)20(2)8-6-16-26(3,4)29/h11-12,20,23-25,28-29H,1,6-10,13-18H2,2-5H3/b21-11+,22-12-/t20-,23+,24-,25+,27-/m1/s1
• InChIKey: JWUBBDSIWDLEOM-DTOXIADCSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C[C@H](CCCC(C)(C)O)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](CCC3=C)O)C
  CACTVS 3.341: C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)CCC3=C
  CACTVS 3.341: C[C@H](CCCC(C)(C)O)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3/C[C@@H](O)CCC3=C
  ACDLabs 10.04: OC3CC(=C/C=C1\CCCC2(C)C(C(C)CCCC(O)(C)C)CCC12)/C(=C)CC3
  OpenEye OEToolkits 1.5.0: CC(CCCC(C)(C)O)C1CCC2C1(CCCC2=CC=C3CC(CCC3=C)O)C
• Formula: C27 H44 O2
• Name: 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL;
  25-HYDROXYVITAMIN D3
• ChEMBL: CHEMBL1040
• DrugBank: DB00146
• ZINC: ZINC000004474414
• PDB chain: 5ien Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ien Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold.
• Resolution: 2.089 Å
• Binding residue (original residue number in PDB): F15 L58 Y104 E106 L125
• Binding residue (residue number reindexed from 1): F14 L57 Y103 E105 L124
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=6.52,Kd~300nM

External links

• PDB: RCSB:5ien, PDBe:5ien, PDBj:5ien
• PDBsum: 5ien
• PubMed: 30566669