Comparative Analysis of Pembrolizumab and PD-1 Receptor Binding Properties

Pembrolizumab bound to PD1

Immunotherapy is the treatment of cancer using antibodies that target points of failure in the life cycle of cancer cells. Many of these therapies involve altering monoclonal antibodies to target specific proteins associated with different types of cancer. Understanding the binding properties of these proteins is of utmost importance.

Pembrolizumab, an igG4 Monoclonal Antibody

Some IgG4 antibodies exhibit unusual surface properties that impact their therapeutic function. Pembrolizumab (KEYTRUDA®) is one of these immunotherapies.

Protein Description

Pembrolizumab is a compact antibody used in the treatment of various cancers, most notably indicated for use when EGFR inhibitors fail to reach treatment outcomes. Scientists identified the programmed cell death 1 receptor, PD-1, a protective mechanism on the surface of cancer cells. Pembrolizumab binds to this receptor allowing for the immune system cells to successfully recognize and destroy cancer cells.

Mechanism of Action: PD-1 an Immune Checkpoint

PD-1 receptors are located on the surface of lymphocytes. By avoiding detection from the immune system, binding to other ligands besides our immune system’s antibodies, this receptor prolongs the life of cancer cells. The chemical signal associated to PD-1 is referred to as an “Immune Checkpoint” since the lack of it prevents cellular destruction.

Analysis of binding properties of PD-1 bound to PD-L1

Examination of protein dataset 4ZQK reveals the mechanism of ligand-receptor binding. PD-L1 fits into a U-shaped fold of the PD-1 receptor. Interesting to note that the active sites listed in the dataset are not located in the ligand-receptor binding region. Instead, alternating amino acids from each protein fit together as they find stable connectivity like teeth of a zipper. Without clear active-site ligand binding, it’s possible this conformation is further stabilized by thermic and hydrophobicity congruity of each protein.

Pembrolizumab, an Asymmetrical Monoclonal Antibody

Standard Monoclonal Antibody

Most monoclonal antibodies are known to be symmetrical, with identical FAB fragments. This makes them powerful regulators of surface receptors, many of which form dimers in order to transmit signals.

Monoclonal antibodies are uniquely structured to engage multiple antigens, making it a potent therapeutic compound. Pembrolizumab appears to be structurally different than other monoclonal antibodies, adopting an irregular conformation.

Unique Surface Properties of Pembrolizumab Determine PD-1 Binding

In data-set 5DK3, the Pembrolizumab’s Fc domain is rotated about the central axis towards one of the FAB fragments. The Fc domain has a single CH2 domain rotated 120 degrees off center. The thin connecting region between the FAB and Fc domains are contracted into a central core of the protein, opening up the Fc domain for enhanced binding properties.

Pembrolizumab, IgG4, antibody, biologic models, oncology

Pembrolizumab visualization

To determine the unique surface properties driving the conformation shown in dataset 5DK3, I’ve investigated three things:

  1. An analysis of different surface properties may yield insights into the binding potential of PD-1.
  2. Conduct a comparative analysis of dataset 5dk3 to 5GGS.
  3. Construct a macromolecular complex of an entire antibody bound to cancer-causing receptor.

1. Analysis of Pembrolizumab Surface Properties

Protein behaviors are defined by more than just active sites or amino acid mutations. Conformational states of the protein show us the mechanics of a protein’s function. Interpretation of “active” and “inactive” states of proteins demonstrate the range of movement possible in the protein.

A protein’s surface properties help define how proteins interacts with surrounding molecules. Here, I’ve selected 3 primary modalities to gain insights into Pembrolizumab’s asymmetrical structure, hydrophobicity, Coulumbic, and bFactor.

The hydrophobicity appears uniform throughout the entire protein. As a soluble antibody, its affinity for water is higher and as expected more blue (phillic) than red (phobic).

The Coulumbic property visualizes the electrostatic potential of the protein. Its positive-neutral-negative charge is visualized in blue-white-red. The variation in this surface pattern appears to have a slightly more negative charge on the left where there is the greatest angle between FAB fragment and Fc domain.

Visualization modalities of Pembrolizumab

Finally, bFactor visualizes the protein’s thermic properties, its atomic temperature (red is hot, blue is cool). Here we see clear increased temperature within the extended FAB domain region. This is the same region of the protein identified with a more negative charge by Coulombic analysis.

2. Pembrolizumab FAB Fragment Bound to PD-1

As of the time of publication, no data set of Pembrolizumab exists with a complete antibody bound to one of its antigens. To understand how the entirety of the marco-molecule may behave in the presence of PD-1, a theoretical model of that protein complex can yield insights otherwise hidden within the data.

Visualization of binding residues of PD-1 to Pembrolizumab’s FAB Fragment

PDB dataset: 5GGS contains the 3D atomic structure of Pembrolizumab’s FAB fragment bound to the PD-1 receptor. In this dataset, we can see the exact amino acids involved with binding antigens like PD-1. Again we see similar binding properties of PD-1 to PD-L1.

Standard identification of active residues did not locate amino acids of Pembrolizumab and therefore required a visual inspection to identify which residues most likely involved. There were no clear Pembrolizumab–PD-1 bonds, but rather the same zipper-like alternating amino acids of the two proteins seen in dataset 4ZQK.

While Pembrolizumab and PD-L1 share similar mechanisms for binding, Pembrolizumab does not bind to the same U-shaped region of PD-1. While close, it engages different residues near those engaged by PD-L1, but not the same. It would be interesting to see if other Anti-PD1 antibodies bind to the same PD-1 residues.

3. Macromolecular assembly of Pembrolizumab / PD-1 Complex

To further understand the binding properties of Pembrolizumab, it would be interesting to understand how the complete antibody would correlate to the now understood binding configuration of its FAB fragment to PD-1.

Since Pembrolizumab is a monoclonal antibody, protein dataset 5GGS is an ideal model to use for alignment of PD-1 to the FAB domains of our complete Pembrolizumab model.

Composite model of Pembrolizumab bound to PD-1

Here we can see 5GGS aligned to the contracted FAB fragment of 5DK3. Since this is a monoclonal antibody, the alignment of 5GGS on one FAB fragments should be symmetrical to the other side.

Determining if both FAB Regions Bind Antigen

As expected, both FAB / PD-1 models from 5GGS align nicely to the FAB domains of Pembrolizumab. It would seem very likely that the antibody capable of binding two antigens simultaneously. Should this be the case, the thermic properties of each should yield clues about that potential binding.

Analysis of surface properties of Pembrolizumab to multiple PD-1 receptors

Upon further inspection, there’s thermic discongruity on the extended FAB domain of the antibody where it would interface with PD-1. As noted, one side expresses an increased atomic temperature while the other cooler with more thermic affinity to PD-1. This may pose a complication for symmetrical binding of PD-1. Pembrolizumab is mutated at C228P to prevent Fc domain binding. This mitigates antob0dy-dependent cell-mediated cytotoxicity.  Those residues are located at the intersection of the FAB fragments and Fc domain. The Fc domain also shows more thermic activity on the extended surface of the Antibody. As such, it seems possible that the extended FAB fragment may also share the Fc domains disinterest in binding to antigens or receptors.


Monoclonal antibodies like Pembrolizumab show enormous promise for a patient-specific targeting of cancer cells. The science behind immunotherapy is as fascinating as it is beautiful.

When considering the macro-molecular structure of PD-1 bound to Pembrolizumab, the surface properties of receptor-to-antibody may play an important role in determining the binding orientation of Pembrolizumab to the plasma membrane. Due to the asymmetrical alignment of this antibody, this may, in fact, present therapeutic advantages.

Purchase Protein Models

If you liked reading this article and would enjoy exploring Pembrolizumab’s unique structure by hand, you can purchase a 3D print of Pembrolizumab bound to PD-1. Models are available in multiple sizes.


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