Structure of PDB 5niu Chain D Binding Site BS01

Receptor Information

>5niu Chain D (length=127) Species: 9606 (Homo sapiens)

AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQF
VHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMIS
YGGADYKRITVKVNAPYAAALEHHHHH

Ligand information

• Ligand ID: 8YZ
• InChI: InChI=1S/C35H34N2O7/c1-22-13-28(18-37-30(19-38)35(39)40)33(43-20-25-6-3-5-24(14-25)17-36)16-32(22)44-21-27-7-4-8-29(23(27)2)26-9-10-31-34(15-26)42-12-11-41-31/h3-10,13-16,30,37-38H,11-12,18-21H2,1-2H3,(H,39,40)/t30-/m1/s1
• InChIKey: UWNXGZKSIKQKAH-SSEXGKCCSA-N
• SMILES:
  CACTVS 3.385: Cc1cc(CN[CH](CO)C(O)=O)c(OCc2cccc(c2)C#N)cc1OCc3cccc(c3C)c4ccc5OCCOc5c4
  CACTVS 3.385: Cc1cc(CN[C@H](CO)C(O)=O)c(OCc2cccc(c2)C#N)cc1OCc3cccc(c3C)c4ccc5OCCOc5c4
  OpenEye OEToolkits 2.0.6: Cc1cc(c(cc1OCc2cccc(c2C)c3ccc4c(c3)OCCO4)OCc5cccc(c5)C#N)CNC(CO)C(=O)O
  OpenEye OEToolkits 2.0.6: Cc1cc(c(cc1OCc2cccc(c2C)c3ccc4c(c3)OCCO4)OCc5cccc(c5)C#N)CN[C@H](CO)C(=O)O
• Formula: C35 H34 N2 O7
• Name: (2~{R})-2-[[2-[(3-cyanophenyl)methoxy]-4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]-5-methyl-phenyl]methylamino]-3-oxidanyl-propanoic acid
• ChEMBL: CHEMBL4084368
• PDB chain: 5niu Chain D Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5niu Small-molecule inhibitors of PD-1/PD-L1 immune checkpoint alleviate the PD-L1-induced exhaustion of T-cells.
• Resolution: 2.01 Å
• Binding residue (original residue number in PDB): T20 Y56 M115 A121 D122 Y123 K124
• Binding residue (residue number reindexed from 1): T3 Y39 M98 A104 D105 Y106 K107
• Annotation score: 1
• Binding affinity: BindingDB: IC50=2.3nM

External links

• PDB: RCSB:5niu, PDBe:5niu, PDBj:5niu
• PDBsum: 5niu
• PubMed: 29069777
• UniProt: Q9NZQ7|PD1L1_HUMAN Programmed cell death 1 ligand 1 (Gene Name=CD274)