Structure of PDB 6tol Chain A Binding Site BS01

Receptor Information
>6tol Chain A (length=130) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LYFQGADSCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTV
LMACSGLFYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLRE
GNIMAVMATAMYLQMEHVVDTCRKFIKASE
Ligand information
Ligand IDNQW
InChIInChI=1S/C23H31ClN6O3/c1-14-12-29(13-15(2)33-14)21-25-11-17(24)20(27-21)26-16-6-7-18-19(10-16)30(22(31)28(18)5)9-8-23(3,4)32/h6-7,10-11,14-15,32H,8-9,12-13H2,1-5H3,(H,25,26,27)/t14-,15+
InChIKeyJPAZTMKUVSFPAZ-GASCZTMLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[C@@H]1CN(C[C@@H](O1)C)c2ncc(c(n2)Nc3ccc4c(c3)N(C(=O)N4C)CCC(C)(C)O)Cl
OpenEye OEToolkits 2.0.7CC1CN(CC(O1)C)c2ncc(c(n2)Nc3ccc4c(c3)N(C(=O)N4C)CCC(C)(C)O)Cl
CACTVS 3.385C[CH]1CN(C[CH](C)O1)c2ncc(Cl)c(Nc3ccc4N(C)C(=O)N(CCC(C)(C)O)c4c3)n2
CACTVS 3.385C[C@@H]1CN(C[C@H](C)O1)c2ncc(Cl)c(Nc3ccc4N(C)C(=O)N(CCC(C)(C)O)c4c3)n2
FormulaC23 H31 Cl N6 O3
Name5-[[5-chloranyl-2-[(2~{S},6~{R})-2,6-dimethylmorpholin-4-yl]pyrimidin-4-yl]amino]-1-methyl-3-(3-methyl-3-oxidanyl-butyl)benzimidazol-2-one
ChEMBLCHEMBL4476234
DrugBank
ZINC
PDB chain6tol Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6tol AchievingIn VivoTarget Depletion through the Discovery and Optimization of Benzimidazolone BCL6 Degraders.
Resolution1.64 Å
Binding residue
(original residue number in PDB)
M51 A52 C53 G55 Y58 Q113 E115
Binding residue
(residue number reindexed from 1)
M52 A53 C54 G56 Y59 Q114 E116
Annotation score1
Binding affinityMOAD: ic50=0.15uM
BindingDB: IC50=150nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6tol, PDBe:6tol, PDBj:6tol
PDBsum6tol
PubMed32275432
UniProtP41182|BCL6_HUMAN B-cell lymphoma 6 protein (Gene Name=BCL6)

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