Structure of PDB 8jba Chain B Binding Site BS01

Receptor Information

>8jba Chain B (length=125) Species: 9606 (Homo sapiens)

AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQF
VHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMIS
YGGADYKRITVKVNAPYAAALEHHH

Ligand information

• Ligand ID: AU9
• InChI: InChI=1S/C27H27N3O5S/c1-18-22(21-9-3-2-4-10-21)11-6-12-24(18)34-16-25-29-30-27(35-25)36-17-20-8-5-7-19(13-20)14-28-23(15-31)26(32)33/h2-13,23,28,31H,14-17H2,1H3,(H,32,33)/t23-/m0/s1
• InChIKey: AAJMOHIHVOUUDE-QHCPKHFHSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: Cc1c(cccc1OCc2nnc(o2)SCc3cccc(c3)CNC(CO)C(=O)O)c4ccccc4
  CACTVS 3.385: Cc1c(OCc2oc(SCc3cccc(CN[CH](CO)C(O)=O)c3)nn2)cccc1c4ccccc4
  CACTVS 3.385: Cc1c(OCc2oc(SCc3cccc(CN[C@@H](CO)C(O)=O)c3)nn2)cccc1c4ccccc4
  OpenEye OEToolkits 2.0.7: Cc1c(cccc1OCc2nnc(o2)SCc3cccc(c3)CN[C@@H](CO)C(=O)O)c4ccccc4
• Formula: C27 H27 N3 O5 S
• Name: (2~{S})-2-[[3-[[5-[(2-methyl-3-phenyl-phenoxy)methyl]-1,3,4-oxadiazol-2-yl]sulfanylmethyl]phenyl]methylamino]-3-oxidanyl-propanoic acid
• PDB chain: 8jba Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8jba Discovery and Crystallography Study of Novel Biphenyl Ether and Oxadiazole Thioether (Non-Arylmethylamine)-Based Small-Molecule PD-1/PD-L1 Inhibitors as Immunotherapeutic Agents.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): I54 Y56 M115 S117 A121 D122 Y123 K124 R125
• Binding residue (residue number reindexed from 1): I37 Y39 M98 S100 A104 D105 Y106 K107 R108
• Annotation score: 1

External links

• PDB: RCSB:8jba, PDBe:8jba, PDBj:8jba
• PDBsum: 8jba
• PubMed: 37674362
• UniProt: Q9NZQ7|PD1L1_HUMAN Programmed cell death 1 ligand 1 (Gene Name=CD274)