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- PDB-9hjg: Crystal structure of human CD73 (ecto-5'-nucleotidase) in complex... -

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Basic information

Entry
Database: PDB / ID: 9hjg
TitleCrystal structure of human CD73 (ecto-5'-nucleotidase) in complex with an N6-disubstituted acyclic ADP analog (compound 26 in publication) in the closed state
Components5'-nucleotidase
KeywordsHYDROLASE / nucleotide analog / dimetal center / closed state
Function / homology
Function and homology information


thymidylate 5'-phosphatase / : / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / adenosine biosynthetic process / inhibition of non-skeletal tissue mineralization / Pyrimidine catabolism / AMP catabolic process ...thymidylate 5'-phosphatase / : / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / adenosine biosynthetic process / inhibition of non-skeletal tissue mineralization / Pyrimidine catabolism / AMP catabolic process / : / IMP-specific 5'-nucleotidase / : / Nicotinate metabolism / Purine catabolism / 5'-nucleotidase / 5'-nucleotidase activity / leukocyte cell-cell adhesion / DNA metabolic process / response to ATP / Purinergic signaling in leishmaniasis infection / ATP metabolic process / calcium ion homeostasis / negative regulation of inflammatory response / external side of plasma membrane / nucleotide binding / cell surface / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsStrater, N. / Moschuetz, S. / Federico, S. / Renn, C. / Muller, C.E.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)335447717 Germany
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Acyclic purine and pyrimidine nucleotide analogs as ecto-5'-nucleotidase (CD73) inhibitors.
Authors: 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.
History
DepositionNov 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-nucleotidase
B: 5'-nucleotidase
C: 5'-nucleotidase
D: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,32719
Polymers241,6224
Non-polymers2,70615
Water00
1
A: 5'-nucleotidase
B: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1449
Polymers120,8112
Non-polymers1,3337
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-112 kcal/mol
Surface area40010 Å2
2
C: 5'-nucleotidase
D: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,18410
Polymers120,8112
Non-polymers1,3738
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-122 kcal/mol
Surface area39760 Å2
Unit cell
Length a, b, c (Å)93.593, 84.551, 124.667
Angle α, β, γ (deg.)90.00, 102.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
5'-nucleotidase / 5'-NT / 5'-deoxynucleotidase / Ecto-5'-nucleotidase / IMP-specific 5'-nucleotidase / Thymidylate 5'- ...5'-NT / 5'-deoxynucleotidase / Ecto-5'-nucleotidase / IMP-specific 5'-nucleotidase / Thymidylate 5'-phosphatase


Mass: 60405.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, NT5, NTE / Production host: Homo sapiens (human)
References: UniProt: P21589, thymidylate 5'-phosphatase, 5'-nucleotidase, 5'-deoxynucleotidase, 7-methylguanosine nucleotidase, IMP-specific 5'-nucleotidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-A1IVH / [5-[2-chloranyl-6-[methyl-(phenylmethyl)amino]purin-9-yl]pentoxy-oxidanyl-phosphoryl]methylphosphonic acid


Mass: 517.840 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H26ClN5O6P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 6000 and 0.1 M Hepes pH 7.0, 10 microM ZnCl2, 10 mM inhibitor and 10 % PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.31→121.66 Å / Num. obs: 36814 / % possible obs: 83.5 % / Redundancy: 6 % / Biso Wilson estimate: 26.4 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.364 / Rpim(I) all: 0.161 / Rrim(I) all: 0.399 / Net I/σ(I): 4.6
Reflection shellResolution: 2.31→2.67 Å / Rmerge(I) obs: 1.018 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1773 / CC1/2: 0.697 / Rpim(I) all: 0.453 / Rrim(I) all: 1.116

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→121.66 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2711 1777 4.83 %
Rwork0.2368 --
obs0.2385 36783 44.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→121.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16262 0 143 0 16405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616764
X-RAY DIFFRACTIONf_angle_d0.8122713
X-RAY DIFFRACTIONf_dihedral_angle_d12.9696271
X-RAY DIFFRACTIONf_chiral_restr0.0512508
X-RAY DIFFRACTIONf_plane_restr0.0072959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.370.380490.3335198X-RAY DIFFRACTION3
2.37-2.440.4581140.3314268X-RAY DIFFRACTION5
2.44-2.520.2978210.3133374X-RAY DIFFRACTION6
2.52-2.610.3944270.3134481X-RAY DIFFRACTION8
2.61-2.720.4454310.3438692X-RAY DIFFRACTION11
2.72-2.840.3104550.31661196X-RAY DIFFRACTION20
2.84-2.990.3444920.31251873X-RAY DIFFRACTION31
2.99-3.180.34991630.30192979X-RAY DIFFRACTION49
3.18-3.420.34012410.28724495X-RAY DIFFRACTION74
3.42-3.770.3032240.25974562X-RAY DIFFRACTION74
3.77-4.310.27772770.22115584X-RAY DIFFRACTION91
4.31-5.430.20473310.19326083X-RAY DIFFRACTION99
5.43-121.660.23012920.2056221X-RAY DIFFRACTION99

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