Structure of PDB 5n1z Chain A Binding Site BS01

Receptor Information

>5n1z Chain A (length=123) Species: 9606 (Homo sapiens)

DSQIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSG
LFYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAV
MATAMYLQMEHVVDTCRKFIKAS

Ligand information

• Ligand ID: 8GQ
• InChI: InChI=1S/C25H25N7O4/c26-11-16-12-27-32-22-10-21(29-25(16)32)31-13-19(9-18(31)14-33)35-5-1-2-6-36-20-8-17(28-22)7-15-3-4-23(34)30-24(15)20/h1-2,7-8,10,12,18-19,28,33H,3-6,9,13-14H2,(H,30,34)/b2-1+/t18-,19-/m0/s1
• InChIKey: SABLEOBBNNRHAD-WNJMFGOSSA-N
• SMILES:
  CACTVS 3.385: OC[C@@H]1C[C@H]2C[N@@]1c3cc(Nc4cc5CCC(=O)Nc5c(OC\C=C\CO2)c4)n6ncc(C#N)c6n3
  OpenEye OEToolkits 2.0.6: c1c2cc(c3c1CCC(=O)N3)OC/C=C/CO[C@H]4C[C@H](N(C4)c5cc(n6c(n5)c(cn6)C#N)N2)CO
  CACTVS 3.385: OC[CH]1C[CH]2C[N]1c3cc(Nc4cc5CCC(=O)Nc5c(OCC=CCO2)c4)n6ncc(C#N)c6n3
  OpenEye OEToolkits 2.0.6: c1c2cc(c3c1CCC(=O)N3)OCC=CCOC4CC(N(C4)c5cc(n6c(n5)c(cn6)C#N)N2)CO
• Formula: C25 H25 N7 O4
• Name: pyrazolo-pyrimidine macrocycle
• ChEMBL: CHEMBL4094351
• PDB chain: 5n1z Chain A Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5n1z Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors.
• Resolution: 1.81 Å
• Binding residue (original residue number in PDB): M51 A52 G55 Y58 Q113 M114 E115
• Binding residue (residue number reindexed from 1): M46 A47 G50 Y53 Q108 M109 E110
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.0065uM
  PDBbind-CN: -logKd/Ki=8.19,Kd=0.0065uM
  BindingDB: IC50=1995nM

External links

• PDB: RCSB:5n1z, PDBe:5n1z, PDBj:5n1z
• PDBsum: 5n1z
• PubMed: 28485934
• UniProt: P41182|BCL6_HUMAN B-cell lymphoma 6 protein (Gene Name=BCL6)