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- PDB-7jv9: Human CD73 (ecto 5'-nucleotidase) in complex with compound 12 -

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Basic information

Entry
Database: PDB / ID: 7jv9
TitleHuman CD73 (ecto 5'-nucleotidase) in complex with compound 12
Components5'-nucleotidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 5'-NUCLEOTIDASE / HYDROLASE / PHOSPHATASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


thymidylate 5'-phosphatase / thymidylate 5'-phosphatase activity / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / inhibition of non-skeletal tissue mineralization / adenosine biosynthetic process / Pyrimidine catabolism / AMP catabolic process ...thymidylate 5'-phosphatase / thymidylate 5'-phosphatase activity / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / inhibition of non-skeletal tissue mineralization / adenosine biosynthetic process / Pyrimidine catabolism / AMP catabolic process / GMP 5'-nucleotidase activity / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / Nicotinate metabolism / Purine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / DNA metabolic process / leukocyte cell-cell adhesion / response to ATP / response to inorganic substance / calcium ion homeostasis / Purinergic signaling in leishmaniasis infection / ATP metabolic process / negative regulation of inflammatory response / external side of plasma membrane / nucleotide binding / cell surface / extracellular exosome / zinc ion binding / nucleoplasm / membrane / identical protein binding / 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 / Chem-VPG / 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGibbons, P. / Du, X.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Orally Bioavailable Small-Molecule CD73 Inhibitor (OP-5244) Reverses Immunosuppression through Blockade of Adenosine Production.
Authors: Du, X. / Moore, J. / Blank, B.R. / Eksterowicz, J. / Sutimantanapi, D. / Yuen, N. / Metzger, T. / Chan, B. / Huang, T. / Chen, X. / Chen, Y. / Duong, F. / Kong, W. / Chang, J.H. / Sun, J. / ...Authors: Du, X. / Moore, J. / Blank, B.R. / Eksterowicz, J. / Sutimantanapi, D. / Yuen, N. / Metzger, T. / Chan, B. / Huang, T. / Chen, X. / Chen, Y. / Duong, F. / Kong, W. / Chang, J.H. / Sun, J. / Zavorotinskaya, T. / Ye, Q. / Junttila, M.R. / Ndubaku, C. / Friedman, L.S. / Fantin, V.R. / Sun, D.
History
DepositionAug 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)118,62514
Polymers116,6112
Non-polymers2,01512
Water99155
1
A: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3137
Polymers58,3051
Non-polymers1,0076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3137
Polymers58,3051
Non-polymers1,0076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)231.933, 93.794, 54.922
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / 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: 0 / Auth seq-ID: 25 - 549 / Label seq-ID: 1 - 525

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 / Ecto-5'-nucleotidase


Mass: 58305.348 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, 5'-nucleotidase
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 65 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-VPG / 6-chloro-N-[(2-chlorophenyl)methyl]-1-[5-O-(phosphonomethyl)-beta-D-ribofuranosyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 520.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20Cl2N5O7P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.25
Details: 12.50 %w/v PEG 1500, 0.10M SPG (Succinic Acid, Sodium Dihydrogen Phosphate and Glycine) pH=4.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→115.97 Å / Num. obs: 31804 / % possible obs: 93.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 55.575 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.095 / Rsym value: 0.08 / Χ2: 1.144 / Net I/σ(I): 10.06
Reflection shellResolution: 2.7→2.95 Å / Redundancy: 3.3 % / Num. unique obs: 7483 / CC1/2: 0.998 / Rrim(I) all: 0.518 / Rsym value: 0.439 / % possible all: 96.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TVE

6tve


Resolution: 2.7→115.97 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.876 / SU B: 33.488 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 762 2.4 %RANDOM
Rwork0.2092 ---
obs0.2108 31041 93.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 149.35 Å2 / Biso mean: 57.627 Å2 / Biso min: 20.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å2-0 Å2
2--2.15 Å20 Å2
3----2.41 Å2
Refinement stepCycle: final / Resolution: 2.7→115.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8194 0 110 55 8359
Biso mean--68.03 37.73 -
Num. residues----1050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198332
X-RAY DIFFRACTIONr_bond_other_d0.0050.027785
X-RAY DIFFRACTIONr_angle_refined_deg1.381.97311307
X-RAY DIFFRACTIONr_angle_other_deg1.197317859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16351048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64824.674353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.246151332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9541536
X-RAY DIFFRACTIONr_chiral_restr0.070.21276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219460
X-RAY DIFFRACTIONr_gen_planes_other0.010.021846
Refine LS restraints NCS

Ens-ID: 1 / Number: 32109 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.521 61 -
Rwork0.449 2326 -
all-2387 -
obs--95.94 %
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)
13.5440.5985-0.68862.9343-0.80083.1967-0.1097-0.17440.14940.06840.0311-0.06980.1260.36820.07860.02910.02350.01790.0611-0.01950.089913.501-24.829-7.802
25.1001-0.91591.6872.7026-0.83845.6670.218-0.80230.15240.25070.0413-0.02220.6032-0.3-0.25940.1223-0.0837-0.05540.3131-0.03320.204146.005-26.543-4.631
33.2607-0.33440.21021.8587-0.10044.585-0.0720.10140.0722-0.11050.01010.05740.2691-0.38320.0620.0266-0.0275-0.01510.03730.0070.111897.955-26.056-19.89
44.81940.52770.80472.3519-0.08813.76280.17550.73510.2998-0.3126-0.08130.01040.39220.3205-0.09430.12010.1338-0.0440.31620.03740.211565.734-26.476-23.228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 333
2X-RAY DIFFRACTION2A334 - 549
3X-RAY DIFFRACTION3B25 - 333
4X-RAY DIFFRACTION4B334 - 549

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