Molecule of the Month: PD-1 (Programmed Cell Death Protein 1)
PD-1 and its ligands are a new target for cancer therapy
Inhibiting Immune Response
Exploring the Structure
PD-L1 and Inhibitor
Researchers are also trying to find small molecules that can be used to block the interaction between PD-1 and its ligand proteins. One of the first successes is shown here, the molecule BMS-202 (PDB entry 5j89). It binds to PD-L1, causing it to dimerize. This blocks the site that normally binds to PD-1, as seen in the complex of human PD-1 with PD-L1 (PDB entry 4zqk). To compare these structures in more detail, click on the image for an interactive JSmol.
Topics for Further Discussion
- You can use the Protein Feature View to see which portions of these molecules are included in the PDB entries—for instance, look at the entry for mouse PD-1.
- You can use the NGL viewer to explore the interaction of ligands with proteins—for instance, look at the interaction of BMS-202 with PD-L1.
Related PDB-101 Resources
- Browse Cancer
- Browse Immune System
- Browse Cellular Signaling
- E. I. Buchbinder & A. Desai (2016) CTLA-4 and PD-1 pathways: similarities, differences, and implications of their inhibition. American Journal of Clinical Oncology 39, 98-106.
- 5jxe: Z. Na, S. P. Yeo, S. R. Bharath, M. W. Bowler, E. Balkc, C. I. Wang & H. Song (2016) Structural basis for blocking PD-1-mediated immune suppression by therapeutic antibody pembrolizumab. Cell Research doi: 10.1038/cr.2016.77.
- 5j89: K. M. Zak, P. Grudnik, K. Guzik, B. J. Zieba, B. Musielak, A. Domling, G. Dubin & T. A. Holak (2016) Structural basis for small molecular targeting of the programmed death ligand 1 (PD-L1) Oncotarget 7, 30323-30335.
- 5dk3: G. Scapin, X. Yang, W. W. Prosise, M. McCoy, P. Reichert, J. M. Johnston, R. S. Kashi & C. Strickland (2015) Structure of full-length anti-PD1 therapeutic IgG4 antibody pembrolizumab. Nature Structural and Molecular Biology 22, 953-958.
- 4zqk: K. M. Zak, R. Kitel, S. Przetocka, P. Golik, K. Guzik, B. Musielak, A. Domling, G. Dubin & T. A. Holak (2015) Structure of the complex of human programmed death 1, PD-1, and its ligand PD-L1. Structure 23, 2341-2348.
- 3bp5: E. Lazar-Molnar, Q. Yan, E. Cao, U. Ramagopal, S. G. Nathenson & S. C. Almo (2008) Crystal structure of the complex between programmed death-1 (PD-1) and its ligand PD-L2. Proceedings of the National Academy of Science USA 105: 10483-10488.
- 3bik: D. Y. Lin, Y. Tanaka, M. Iwasaki, A. G. Gittis, H. P. Su, B. Mikami, T. Okasaki, T. Honjo, N. Minato & D. N. Garboczi (2008) The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors. Proceedings of the National Academy of Science USA 105, 3011-3016.
December 2016, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2016_12