Structure of PDB 6rpg Chain B Binding Site BS01

Receptor Information

>6rpg Chain B (length=117) Species: 9606 (Homo sapiens)

AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQF
VHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMIS
YGGADYKRITVKVNAPY

Ligand information

• Ligand ID: KDW
• InChI: InChI=1S/C54H58N8O6/c1-35-17-47(29-57-13-15-61-39(5)63)53(65-31-43-19-41(23-55)25-59-27-43)21-51(35)67-33-45-9-7-11-49(37(45)3)50-12-8-10-46(38(50)4)34-68-52-22-54(66-32-44-20-42(24-56)26-60-28-44)48(18-36(52)2)30-58-14-16-62-40(6)64/h7-12,17-22,25-28,57-58H,13-16,29-34H2,1-6H3,(H,61,63)(H,62,64)
• InChIKey: RNCINFJGGSQEHN-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: Cc1cc(c(cc1OCc2cccc(c2C)c3cccc(c3C)COc4cc(c(cc4C)CNCCNC(=O)C)OCc5cc(cnc5)C#N)OCc6cc(cnc6)C#N)CNCCNC(=O)C
  CACTVS 3.385: CC(=O)NCCNCc1cc(C)c(OCc2cccc(c2C)c3cccc(COc4cc(OCc5cncc(c5)C#N)c(CNCCNC(C)=O)cc4C)c3C)cc1OCc6cncc(c6)C#N
• Formula: C54 H58 N8 O6
• Name: ~{N}-[2-[[4-[[3-[3-[[4-[(2-acetamidoethylamino)methyl]-5-[(5-cyanopyridin-3-yl)methoxy]-2-methyl-phenoxy]methyl]-2-methyl-phenyl]-2-methyl-phenyl]methoxy]-2-[(5-cyanopyridin-3-yl)methoxy]-5-methyl-phenyl]methylamino]ethyl]ethanamide
• ChEMBL: CHEMBL4575618
• PDB chain: 6rpg Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6rpg Design, Synthesis, Evaluation, and Structural Studies ofC2-Symmetric Small Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Protein-Protein Interaction.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): Y56 Q66 M115 I116 S117 A121 D122 Y123
• Binding residue (residue number reindexed from 1): Y39 Q49 M98 I99 S100 A104 D105 Y106
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.52,IC50=3.0nM
  BindingDB: IC50=3.0nM,EC50=763nM

External links

• PDB: RCSB:6rpg, PDBe:6rpg, PDBj:6rpg
• PDBsum: 6rpg
• PubMed: 31298541
• UniProt: Q9NZQ7|PD1L1_HUMAN Programmed cell death 1 ligand 1 (Gene Name=CD274)