9HJG | pdb_00009hjg

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 
    0.271 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Acyclic purine and pyrimidine nucleotide analogs as ecto-5'-nucleotidase (CD73) inhibitors.

Federico, S.Renn, C.Brehova, P.Janeba, Z.Moschutz, S.Sylvester, K.Shamleh, R.A.Baburi, H.Zimmermann, H.El-Tayeb, A.Strater, N.Muller, C.E.

(2025) Eur J Med Chem 294: 117653-117653

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117653
  • Primary Citation of Related Structures:  
    9HJG

  • PubMed Abstract: 

    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 N 6 -disubstituted acyclic ADP analog 26 (N 6 -benzyl,N 6 -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 (N 6 -benzyl,N 6 -methyladenine-9-yl)hexyloxydiphosphonate, PSB-24000) which exhibited submicromolar potency at human CD73 (K i 563 nM at soluble CD73; K i 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.


  • Organizational Affiliation
    • PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany; Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, I-34127, Trieste, Italy. Electronic address: sfederico@units.it.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-nucleotidase
A, B, C, D
547Homo sapiensMutation(s): 0 
Gene Names: NT5ENT5NTE
EC: 3.1.3.35 (PDB Primary Data), 3.1.3.5 (PDB Primary Data), 3.1.3.89 (PDB Primary Data), 3.1.3.91 (PDB Primary Data), 3.1.3.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P21589 (Homo sapiens)
Explore P21589 
Go to UniProtKB:  P21589
PHAROS:  P21589
GTEx:  ENSG00000135318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21589
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IVH (Subject of Investigation/LOI)
Query on A1IVH

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
N [auth C],
S [auth D]
[5-[2-chloranyl-6-[methyl-(phenylmethyl)amino]purin-9-yl]pentoxy-oxidanyl-phosphoryl]methylphosphonic acid
C19 H26 Cl N5 O6 P2
OLMZSRUZLJBCCU-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
I [auth B]
J [auth B]
L [auth C]
E [auth A],
F [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
Q [auth D],
R [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
O [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
P [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free:  0.271 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.593α = 90
b = 84.551β = 102.62
c = 124.667γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany335447717

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release