Structure of PDB 6too Chain A Binding Site BS02

Receptor Information
>6too 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 IDNR8
InChIInChI=1S/C18H18ClN5O2/c1-3-12(25)10-24-16-8-11(4-5-15(16)23(2)18(24)26)22-14-6-7-21-17(19)13(14)9-20/h4-8,12,25H,3,10H2,1-2H3,(H,21,22)/t12-/m0/s1
InChIKeyYYQGUWHFXVXQOO-LBPRGKRZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC[C@H](O)CN1C(=O)N(C)c2ccc(Nc3ccnc(Cl)c3C#N)cc12
CACTVS 3.385CC[CH](O)CN1C(=O)N(C)c2ccc(Nc3ccnc(Cl)c3C#N)cc12
OpenEye OEToolkits 2.0.7CC[C@@H](CN1c2cc(ccc2N(C1=O)C)Nc3ccnc(c3C#N)Cl)O
OpenEye OEToolkits 2.0.7CCC(CN1c2cc(ccc2N(C1=O)C)Nc3ccnc(c3C#N)Cl)O
FormulaC18 H18 Cl N5 O2
Name2-chloranyl-4-[[1-methyl-3-[(2~{S})-2-oxidanylbutyl]-2-oxidanylidene-benzimidazol-5-yl]amino]pyridine-3-carbonitrile
ChEMBLCHEMBL4550911
DrugBank
ZINC
PDB chain6too 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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PDB6too AchievingIn VivoTarget Depletion through the Discovery and Optimization of Benzimidazolone BCL6 Degraders.
Resolution1.53 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=5.4uM
BindingDB: IC50=4600nM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6too, PDBe:6too, PDBj:6too
PDBsum6too
PubMed32275432
UniProtP41182|BCL6_HUMAN B-cell lymphoma 6 protein (Gene Name=BCL6)

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