9EO0

Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1

• PDB DOI: https://doi.org/10.2210/pdb9EO0/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-14 Released: 2024-06-19 
• Deposition Author(s): Plewka, J., Hec, A., Sitar, T., Holak, T.
• Funding Organization(s): National Center for Research and Development (Poland)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.302 
• R-Value Work: 0.253 

Literature

Nonsymmetrically Substituted 1,1′-Biphenyl-Based Small Molecule Inhibitors of the PD-1/PD-L1 Interaction

Hec-Galazka, A., Tyrcha, U., Barczynski, J., Bielski, P., Mikitiuk, M., Gudz, G.P., Kitel, R., Musielak, B., Plewka, J., Sitar, T., Holak, T.A.

(2024) ACS Med Chem Lett 

• DOI: https://doi.org/10.1021/acsmedchemlett.4c00042

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 91.8 kDa 
• Atom Count: 5,833 
• Modelled Residue Count: 711 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	A, B, C, D, E, F	131	Homo sapiens	Mutation(s): 0  Gene Names: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ7 (Homo sapiens) Explore Q9NZQ7  Go to UniProtKB:  Q9NZQ7
PHAROS:  Q9NZQ7 GTEx:  ENSG00000120217

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H56 (Subject of Investigation/LOI)	G [auth B], H [auth C], J [auth D]	~{N}-[3-[3-[[5-[(2-hydroxyethylamino)methyl]pyridin-2-yl]carbonylamino]-2-methyl-phenyl]-2-methyl-phenyl]-5-[[3-(methylsulfonylamino)propylamino]methyl]pyridine-2-carboxamide C34 H41 N7 O5 S DLMVYWVXLURSSE-UHFFFAOYSA-N
SO4	I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.302 
• R-Value Work: 0.253 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.753	α = 90
b = 75.405	β = 97.249
c = 75.923	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Plewka, J., Hec, A., Sitar, T., Holak, T.

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Funding Organization	Location	Grant Number
National Center for Research and Development (Poland)	Poland	POIR.01.01.01-00-0129/18

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release