Structure of PDB 5mw2 Chain A Binding Site BS01

Receptor Information

>5mw2 Chain A (length=122) Species: 9606 (Homo sapiens)

SQIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGL
FYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAVM
ATAMYLQMEHVVDTCRKFIKAS

Ligand information

• Ligand ID: U52
• InChI: InChI=1S/C24H29ClN6O3/c1-14-7-15(2)12-31(11-14)24-27-10-18(25)22(29-24)28-17-5-6-19-16(8-17)9-20(23(33)30(19)4)34-13-21(32)26-3/h5-6,8-10,14-15H,7,11-13H2,1-4H3,(H,26,32)(H,27,28,29)/t14-,15+
• InChIKey: GXTJETQFYHZHNB-GASCZTMLSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC1CC(CN(C1)c2ncc(c(n2)Nc3ccc4c(c3)C=C(C(=O)N4C)OCC(=O)NC)Cl)C
  CACTVS 3.385: CNC(=O)COC1=Cc2cc(Nc3nc(ncc3Cl)N4C[CH](C)C[CH](C)C4)ccc2N(C)C1=O
  OpenEye OEToolkits 2.0.6: C[C@@H]1C[C@@H](CN(C1)c2ncc(c(n2)Nc3ccc4c(c3)C=C(C(=O)N4C)OCC(=O)NC)Cl)C
  CACTVS 3.385: CNC(=O)COC1=Cc2cc(Nc3nc(ncc3Cl)N4C[C@@H](C)C[C@@H](C)C4)ccc2N(C)C1=O
• Formula: C24 H29 Cl N6 O3
• Name: 2-[6-[[5-chloranyl-2-[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]pyrimidin-4-yl]amino]-1-methyl-2-oxidanylidene-quinolin-3-yl]oxy-~{N}-methyl-ethanamide
• ChEMBL: CHEMBL4640049
• PDB chain: 5mw2 Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mw2 Chemically Induced Degradation of the Oncogenic Transcription Factor BCL6.
• Resolution: 2.35 Å
• Binding residue (original residue number in PDB): M51 A52 C53 G55 Y58 F89 Q113 M114 E115 H116 V117
• Binding residue (residue number reindexed from 1): M45 A46 C47 G49 Y52 F83 Q107 M108 E109 H110 V111
• Annotation score: 1
• Binding affinity: MOAD: ic50<3nM
  PDBbind-CN: -logKd/Ki=8.52,IC50<3nM

External links

• PDB: RCSB:5mw2, PDBe:5mw2, PDBj:5mw2
• PDBsum: 5mw2
• PubMed: 28930682
• UniProt: P41182|BCL6_HUMAN B-cell lymphoma 6 protein (Gene Name=BCL6)