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- PDB-9r0h: Human CD73 (ecto 5'-nucleotidase) in complex with compound 6 (ORI... -

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Basic information

Entry
Database: PDB / ID: 9r0h
TitleHuman CD73 (ecto 5'-nucleotidase) in complex with compound 6 (ORIC-533)
Components5'-nucleotidase
KeywordsHYDROLASE / 5'-NUCLEOTIDASE / PHOSPHATASE / INHIBITOR
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
: / PHOSPHATE ION / 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsMoore, J.T. / Ivic, N. / Lammens, A. / Krapp, S. / Maskos, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of ORIC-533, an Orally Bioavailable CD73 Inhibitor That Maintains Activity in High AMP Environments to Reverse Tumor Immunosuppression.
Authors: Moore, J.T. / Kawai, H. / Blank, B.R. / Wu, K. / Yeh, C.H. / Zhu, L. / Pham, J.D. / Rew, Y. / Eksterowicz, J. / Salaniwal, S. / Sutimantanapi, D. / Warne, R. / Yuen, N. / Metzger, T.C. / ...Authors: Moore, J.T. / Kawai, H. / Blank, B.R. / Wu, K. / Yeh, C.H. / Zhu, L. / Pham, J.D. / Rew, Y. / Eksterowicz, J. / Salaniwal, S. / Sutimantanapi, D. / Warne, R. / Yuen, N. / Metzger, T.C. / Chan, B. / Huang, T. / Chen, X. / Chen, Y. / Duong, F. / Kong, W. / Chang, J.H. / Sun, J.D. / Zavorotinskaya, T. / Ye, Q. / Al-Sayah, M.A. / Jackson, E. / Junttila, M.R. / Fantin, V.R. / Ndubaku, C.O. / Sun, D. / Du, X. / Friedman, L.S.
History
DepositionApr 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,22914
Polymers118,6372
Non-polymers2,59212
Water8,035446
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-64 kcal/mol
Surface area41980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.962, 93.030, 54.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-839-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 25 - 549 / Label seq-ID: 3 - 527

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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: 59318.484 Da / Num. of mol.: 2 / Mutation: N53D, N333D, N403D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5E, NT5, NTE / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: P21589, thymidylate 5'-phosphatase, 5'-nucleotidase, 5'-deoxynucleotidase, 7-methylguanosine nucleotidase, IMP-specific 5'-nucleotidase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 456 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-A1JCH / [(2~{S})-2-[[(2~{R},3~{S},4~{R},5~{R})-5-[6-chloranyl-4-(cyclopentylamino)pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]-1-oxidanyl-3-(1~{H}-1,2,3,4-tetrazol-5-ylmethoxy)propan-2-yl]phosphonic acid


Mass: 605.926 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29ClN9O9P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: SPG buffer 0.1M pH4.0, 15% Peg 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.28→115.48 Å / Num. obs: 54311 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / CC1/2: 0.998 / Rrim(I) all: 0.087 / Net I/σ(I): 14.44
Reflection shellResolution: 2.28→2.53 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.43 / Num. unique obs: 14403 / % possible all: 99.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0155refinement
REFMACphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→115.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.903 / SU B: 14.274 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 1327 2.4 %RANDOM
Rwork0.19816 ---
obs0.19942 52983 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.449 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å2-0 Å2-0 Å2
2--0.5 Å2-0 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.28→115.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8199 0 152 446 8797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198525
X-RAY DIFFRACTIONr_bond_other_d0.0030.027995
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.96811571
X-RAY DIFFRACTIONr_angle_other_deg1.294318416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06151062
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78724.722360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.712151396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4831537
X-RAY DIFFRACTIONr_chiral_restr0.0920.21298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219595
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021866
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8772.3074242
X-RAY DIFFRACTIONr_mcbond_other1.8742.3054239
X-RAY DIFFRACTIONr_mcangle_it2.7843.885302
X-RAY DIFFRACTIONr_mcangle_other2.7843.8825303
X-RAY DIFFRACTIONr_scbond_it3.2522.7874283
X-RAY DIFFRACTIONr_scbond_other3.2272.7774276
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5844.5416258
X-RAY DIFFRACTIONr_long_range_B_refined7.44522.329040
X-RAY DIFFRACTIONr_long_range_B_other7.45122.0448983
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12478 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 91 -
Rwork0.278 3868 -
obs--99.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.62120.6958-0.26742.4166-0.52991.5360.0165-0.04210.12150.2073-0.00130.0241-0.0830.0691-0.01530.11260.00670.00480.2625-0.01170.006312.644-24.267-8.086
24.8505-0.79421.0372.2267-0.50353.28150.0833-0.57930.26470.2047-0.0055-0.2110.0092-0.0416-0.07790.1153-0.0474-0.04030.4649-0.04540.120745.021-25.713-4.646
32.4925-0.3247-0.09721.68530.42182.3372-0.0070.12040.1051-0.0733-0.06170.02370.0412-0.06150.06870.0853-0.0037-0.00950.28090.01230.012496.984-25.908-19.448
44.60230.49010.81241.99130.22632.62920.11190.46470.2637-0.1765-0.06170.13830.05320.0415-0.05010.12220.0539-0.03970.44170.00440.124664.748-26.072-22.941
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 333
2X-RAY DIFFRACTION2A334 - 599
3X-RAY DIFFRACTION3B1 - 333
4X-RAY DIFFRACTION4B334 - 599

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