9HD5 | pdb_00009hd5

Crystal structure of CD73 (ecto-5'-nucleotidase) in complex with the AOPCP derivative PSB19427 in the closed state

• PDB DOI: https://doi.org/10.2210/pdb9HD5/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-11-11 Released: 2025-11-19 
• Deposition Author(s): Strater, N., Moschuetz, S., Dobelmann, C., Schmies, C.C., Jacobson, K.A., Muller, C.E., Junker, A.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.273 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Positron emission tomography (PET) tracer enables imaging of CD73 expression in cancer

Dobelmann, C., Schmies, C.C.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 121.4 kDa 
• Atom Count: 8,195 
• Modeled Residue Count: 1,026 
• Deposited Residue Count: 1,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-nucleotidase	A, B	542	Homo sapiens	Mutation(s): 0  Gene Names: NT5E, NT5, NTE 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IT6 (Subject of Investigation/LOI)	E [auth A], H [auth B]	[[(2~{R},3~{S},4~{R},5~{R})-5-[2-chloranyl-6-[[4-[1-(2-fluoranylethyl)-1,2,3-triazol-4-yl]phenyl]methyl-propyl-amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid C25 H32 Cl F N8 O9 P2 HUGOUIYDRYRLCG-UMCMBGNQSA-N
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.273 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.635	α = 90
b = 233.367	β = 90
c = 54.058	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Strater, N., Moschuetz, S., Dobelmann, C., Schmies, C.C., Jacobson, K.A., Muller, C.E., Junker, A.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	JU 2966/2-2
German Research Foundation (DFG)	Germany	SFB 1328

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release