PD-1 (Programmed Cell Death Protein 1)

PD-1 and its ligands are a new target for cancer therapy

Interaction of PD-1 with its ligands PD-L1 and PD-L2. The cell membranes are shown schematically in gray, and the portions of the proteins not included in the structure are also shown schematically.
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Our immune system walks a fine line: it needs to fight invaders, but without attacking our own cells in the process. Intelligence is a big part of this fight: MHC gathers information about infections and delivers it to T-cell receptors on the surface of protective cells in the immune system. But the response of the immune system to this information needs to be carefully balanced, so many other molecules tune the process, stimulating and inhibiting the action of MHC and T-cell receptors as necessary.

Inhibiting Immune Response

Several proteins act as checkpoints to slow down T-cells, making sure they are only active when needed. CTLA-4 acts as a checkpoint as T-cells are maturing, while they are still in lymph nodes, and PD-1 (programmed cell death protein 1) acts later, to control overactive T-cells throughout the body. Both are found on the surface of T-cells, and they perform their regulatory function when activated by other immune system cells.

Making Contact

PD-1 extends from the surface of T-cells, and interacts with two similar ligand proteins, PD-L1 and PD-L2, that are found on the surface of regulatory cells such as the cells that present antigens harvested from invaders. Structures have been obtained for the extracellular portions of these molecules, revealing that they all have a similar modular structure, composed of small domains similar in structure to the domains found in antibodies (PDB entries 3bik and 3bp5).

Interaction of PD-1 with the anti-cancer antibody pembrolizumab.
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Fighting Cancer

Cancer cells are adept at evading the immune system. Cancers such as melanomas are thought to do this by expressing PD-L1 on their surface, allowing them to trick the immune system by downregulating T-cells. New treatments have been developed that target these cancer cells by blocking the interaction of PD-1 and PD-L1, restoring T-cell function. The one shown here is pembrolizumab, an antibody that binds to PD-1 and blocks the site that PD-L1 binds (PDB entries 5jxe and 5dk3).

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

  1. 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.
  2. 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.


  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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 Goodsell

About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details. More