Structure of PDB 6toi Chain A Binding Site BS02

Receptor Information
>6toi Chain A (length=125) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADSCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACS
GLFYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLREGNIMA
VMATAMYLQMEHVVDTCRKFIKASE
Ligand information
Ligand IDNQN
InChIInChI=1S/C18H18ClN5O2/c1-11(25)6-8-24-16-9-12(3-4-15(16)23(2)18(24)26)22-14-5-7-21-17(19)13(14)10-20/h3-5,7,9,11,25H,6,8H2,1-2H3,(H,21,22)/t11-/m1/s1
InChIKeyYEBUIPXITBJLFQ-LLVKDONJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(CCN1c2cc(ccc2N(C1=O)C)Nc3ccnc(c3C#N)Cl)O
CACTVS 3.385C[CH](O)CCN1C(=O)N(C)c2ccc(Nc3ccnc(Cl)c3C#N)cc12
OpenEye OEToolkits 2.0.7C[C@H](CCN1c2cc(ccc2N(C1=O)C)Nc3ccnc(c3C#N)Cl)O
CACTVS 3.385C[C@@H](O)CCN1C(=O)N(C)c2ccc(Nc3ccnc(Cl)c3C#N)cc12
FormulaC18 H18 Cl N5 O2
Name2-chloranyl-4-[[1-methyl-3-[(3~{R})-3-oxidanylbutyl]-2-oxidanylidene-benzimidazol-5-yl]amino]pyridine-3-carbonitrile
ChEMBLCHEMBL4550751
DrugBank
ZINC
PDB chain6toi 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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PDB6toi AchievingIn VivoTarget Depletion through the Discovery and Optimization of Benzimidazolone BCL6 Degraders.
Resolution1.58 Å
Binding residue
(original residue number in PDB)		M51 A52 C53 G55 Y58 Q113 E115
Binding residue
(residue number reindexed from 1)		M47 A48 C49 G51 Y54 Q109 E111
Annotation score1
Binding affinityMOAD: ic50=1.7uM
BindingDB: IC50=1700nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6toi, PDBe:6toi, PDBj:6toi
PDBsum6toi
PubMed32275432
UniProtP41182|BCL6_HUMAN B-cell lymphoma 6 protein (Gene Name=BCL6)

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