Structure of PDB 6tom Chain A Binding Site BS01

Receptor Information

>6tom Chain A (length=131) Species: 9606 (Homo sapiens)

NLYFQGADSCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKT
VLMACSGLFYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLR
EGNIMAVMATAMYLQMEHVVDTCRKFIKASE

Ligand information

• Ligand ID: NQZ
• InChI: InChI=1S/C24H31ClF2N6O2/c1-14-12-32(13-15(2)24(14,26)27)21-28-11-17(25)20(30-21)29-16-6-7-18-19(10-16)33(22(34)31(18)5)9-8-23(3,4)35/h6-7,10-11,14-15,35H,8-9,12-13H2,1-5H3,(H,28,29,30)/t14-,15+
• InChIKey: VFNPUAOAEFMXQI-GASCZTMLSA-N
• SMILES:
  CACTVS 3.385: C[CH]1CN(C[CH](C)C1(F)F)c2ncc(Cl)c(Nc3ccc4N(C)C(=O)N(CCC(C)(C)O)c4c3)n2
  OpenEye OEToolkits 2.0.7: CC1CN(CC(C1(F)F)C)c2ncc(c(n2)Nc3ccc4c(c3)N(C(=O)N4C)CCC(C)(C)O)Cl
  CACTVS 3.385: C[C@@H]1CN(C[C@H](C)C1(F)F)c2ncc(Cl)c(Nc3ccc4N(C)C(=O)N(CCC(C)(C)O)c4c3)n2
  OpenEye OEToolkits 2.0.7: C[C@@H]1CN(C[C@@H](C1(F)F)C)c2ncc(c(n2)Nc3ccc4c(c3)N(C(=O)N4C)CCC(C)(C)O)Cl
• Formula: C24 H31 Cl F2 N6 O2
• Name: 5-[[2-[(3~{S},5~{R})-4,4-bis(fluoranyl)-3,5-dimethyl-piperidin-1-yl]-5-chloranyl-pyrimidin-4-yl]amino]-1-methyl-3-(3-methyl-3-oxidanyl-butyl)benzimidazol-2-one
• ChEMBL: CHEMBL4445645
• PDB chain: 6tom Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6tom AchievingIn VivoTarget Depletion through the Discovery and Optimization of Benzimidazolone BCL6 Degraders.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): M51 A52 C53 G55 Y58 Q113
• Binding residue (residue number reindexed from 1): M53 A54 C55 G57 Y60 Q115
• Annotation score: 1
• Binding affinity: MOAD: ic50=0.52uM
  BindingDB: IC50=520nM

External links

• PDB: RCSB:6tom, PDBe:6tom, PDBj:6tom
• PDBsum: 6tom
• PubMed: 32275432
• UniProt: P41182|BCL6_HUMAN B-cell lymphoma 6 protein (Gene Name=BCL6)