9QSM | pdb_00009qsm

small molecule inhibitor in complex with PD-L1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.270 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.244 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

N-terphenylpicolinamide derivatives designed to target PD-L1 increase activation and proliferation of T cells, and their cytotoxic properties toward cancer cells.

Muszak, D.Kocik-Krol, J.Zaber, J.Kruc, O.Palej, U.Fijolkowska, K.Maslanka, A.Magiera-Mularz, K.Plewka, J.Stec, M.Surmiak, M.Szafarz, M.Siedlar, M.Musielak, B.Kitel, R.Wyska, E.Skalniak, L.Surmiak, E.

(2026) Eur J Med Chem 307: 118652-118652

  • DOI: https://doi.org/10.1016/j.ejmech.2026.118652
  • Primary Citation of Related Structures:  
    9QSM

  • PubMed Abstract: 

    Programmed Cell Death Protein-1 (PD-1)/Programmed Cell Death-Ligand 1 (PD-L1) interaction has a crucial role in maintaining the immune system's self-tolerance by downregulating T cell activation. This mechanism is also used by several types of cancers. By overexpressing the PD-L1 protein, cancer cells can evade the immune response and, therefore, become invisible to the immune system. Herein, we present a detailed characterization of the activity of improved N-terphenylpicolinamides, a class of small molecular blockers targeting the PD-L1 protein disclosed in our recent patent and following patent applications. In our studies, we utilized a cell-based structure-activity relationship (SAR) analysis, which allowed us to discriminate the bioactivity of molecules beyond the detection limits of the protein-based HTRF assay. Our final molecules display high affinity to the molecular target and in vitro bioactivity approaching the activity of a positive control ARB-272572 molecule. An optimized molecule activates primary immune cells, leading to enhanced elimination of cancer cells, as we show in a newly developed co-culture setup. In addition, a co-crystal structure described here confirms the intended mode of binding of the small molecule to PD-L1. Our pharmacokinetics (PK) results rationalize the choice of a representative molecule for further in vivo testing.


  • Organizational Affiliation
    • Jagiellonian University, Faculty of Chemistry, Department of Organic Chemistry, Gronostajowa 2, Krakow, 30-387, Poland. Electronic address: damian.muszak@uj.edu.pl.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Programmed cell death 1 ligand 1
A, B, C, D, E
A, B, C, D, E, F
128Homo sapiensMutation(s): 0 
Gene Names: CD274B7H1PDCD1L1PDCD1LG1PDL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ7 (Homo sapiens)
Explore Q9NZQ7 
Go to UniProtKB:  Q9NZQ7
PHAROS:  Q9NZQ7
GTEx:  ENSG00000120217 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZQ7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JAE (Subject of Investigation/LOI)
Query on A1JAE

Download Ideal Coordinates CCD File 
G [auth B],
H [auth D],
I [auth E]
~{N}-[2-chloranyl-3-[2-chloranyl-3-[4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-3-methoxy-phenyl]phenyl]phenyl]-5-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]pyridine-2-carboxamide
C35 H40 Cl2 N4 O8
MMYCKRBDDQKLBL-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.270 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.244 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.521α = 90
b = 74.996β = 95.49
c = 74.614γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePolandUMO-2021/42/E/NZ7/00422
Polish National Science CentrePolandUMO-2020/39/D/ST4/01344

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-18
    Type: Initial release
  • Version 1.1: 2026-02-25
    Changes: Database references