8P64

Co-crystal structure of PD-L1 with low molecular weight inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8P64/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-25 Released: 2024-03-06 
• Deposition Author(s): Plewka, J., Magiera-Mularz, K., van der Straat, R., Draijer, R., Surmiak, E., Butera, R., Land, L., Musielak, B., Domling, A.
• Funding Organization(s): Foundation for Polish Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.297 
• R-Value Work: 0.234 

Literature

1,5-disubstituted Tetrazoles as PD-1/PD-L1 Antagonist

van der Straat, R., Draijer, R., Surmiak, E., Butera, R., Land, L., Magiera-Mularz, K., Musielak, B., Plewka, J., Holak, T., Domling, A.

(2024) RSC Med Chem 

• DOI: https://doi.org/10.1039/D3MD00746D

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.23 kDa 
• Atom Count: 1,799 
• Modelled Residue Count: 235 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	A, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X1Q (Subject of Investigation/LOI)	C [auth B]	~{N}-[[1-[(~{E})-2-(2-methyl-3-phenyl-phenyl)ethenyl]-1,2,3,4-tetrazol-5-yl]methyl]ethanamine C19 H21 N5 WDSZHUIPBINVDD-OUKQBFOZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.297 
• R-Value Work: 0.234 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.45	α = 90
b = 73.45	β = 90
c = 96.08	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Plewka, J., Magiera-Mularz, K., van der Straat, R., Draijer, R., Surmiak, E., Butera, R., Land, L., Musielak, B., Domling, A.

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Funding Organization	Location	Grant Number
Foundation for Polish Science	Poland	POIR.04.04.00-00-420F/17-00

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release