Structure of PDB 5n20 Chain A Binding Site BS01

Receptor Information

>5n20 Chain A (length=123) Species: 9606 (Homo sapiens)

DSQIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSG
LFYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAV
MATAMYLQMEHVVDTCRKFIKAS

Ligand information

• Ligand ID: 8GN
• InChI: InChI=1S/C24H29N9O/c1-15(34)27-20-10-18(6-7-21(20)32-9-8-19(14-32)31(2)3)28-22-11-23(29-17-4-5-17)33-24(30-22)16(12-25)13-26-33/h6-7,10-11,13,17,19,29H,4-5,8-9,14H2,1-3H3,(H,27,34)(H,28,30)/t19-/m1/s1
• InChIKey: PAKOVKWPBKKYGI-LJQANCHMSA-N
• SMILES:
  CACTVS 3.385: CN(C)[C@@H]1CCN(C1)c2ccc(Nc3cc(NC4CC4)n5ncc(C#N)c5n3)cc2NC(C)=O
  OpenEye OEToolkits 2.0.6: CC(=O)Nc1cc(ccc1N2CC[C@H](C2)N(C)C)Nc3cc(n4c(n3)c(cn4)C#N)NC5CC5
  CACTVS 3.385: CN(C)[CH]1CCN(C1)c2ccc(Nc3cc(NC4CC4)n5ncc(C#N)c5n3)cc2NC(C)=O
  OpenEye OEToolkits 2.0.6: CC(=O)Nc1cc(ccc1N2CCC(C2)N(C)C)Nc3cc(n4c(n3)c(cn4)C#N)NC5CC5
• Formula: C24 H29 N9 O
• Name: ~{N}-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-[(3~{R})-3-(dimethylamino)pyrrolidin-1-yl]phenyl]ethanamide
• PDB chain: 5n20 Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5n20 Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors.
• Resolution: 1.38 Å
• Binding residue (original residue number in PDB): M51 A52 C53 S54 Y58 S59
• Binding residue (residue number reindexed from 1): M46 A47 C48 S49 Y53 S54
• Annotation score: 1
• Binding affinity: MOAD: ic50=61uM
  PDBbind-CN: -logKd/Ki=4.21,IC50=61uM

External links

• PDB: RCSB:5n20, PDBe:5n20, PDBj:5n20
• PDBsum: 5n20
• PubMed: 28485934
• UniProt: P41182|BCL6_HUMAN B-cell lymphoma 6 protein (Gene Name=BCL6)