9HJG image
Deposition Date 2024-11-29
Release Date 2025-05-28
Last Version Date 2025-05-28
Entry Detail
PDB ID:
9HJG
Keywords:
Title:
Crystal structure of human CD73 (ecto-5'-nucleotidase) in complex with an N6-disubstituted acyclic ADP analog (compound 26 in publication) in the closed state
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.31 Å
R-Value Free:
0.27
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:5'-nucleotidase
Gene (Uniprot):NT5E
Chain IDs:A, B, C, D
Chain Length:547
Number of Molecules:4
Biological Source:Homo sapiens
Primary Citation
Acyclic purine and pyrimidine nucleotide analogs as ecto-5'-nucleotidase (CD73) inhibitors.
Eur.J.Med.Chem. 294 117653 117653 (2025)
PMID: 40378575 DOI: 10.1016/j.ejmech.2025.117653

Abstact

Ecto-5'-nucleotidase (CD73) is a novel target in cancer (immuno)therapy. Its blockade prevents the formation of immunosuppressive and cancer-promoting adenosine from AMP. Here, we report on the development of a series of small molecules that mimic adenine nucleotides, in which the ribose moiety was replaced by an alkyl chain. Its length was found to be crucial for potency. A crystal structure of the N6-disubstituted acyclic ADP analog 26 (N6-benzyl,N6-methyladenine-9-yl)pentyloxydiphosphonate) in complex with human CD73 revealed that the flexible pentyl linker adopts to interdomain rotation angles differing by up to 18.5°. The most potent CD73 inhibitor of the present series was analog 27 (N6-benzyl,N6-methyladenine-9-yl)hexyloxydiphosphonate, PSB-24000) which exhibited submicromolar potency at human CD73 (Ki 563 nM at soluble CD73; Ki 481 nM at membrane-bound CD73 of triple-negative breast cancer cells). Acyclic nucleotide analogs may be advantageous compared to the previously reported nucleotidic CD73 inhibitors due to their high chemical stability, and because less off-target effects are to be expected. The structure-activity relationships discovered in this study provide valuable insights which will be useful for the development of CD73 inhibitors as immunotherapeutic drugs.

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