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- PDB-5nwh: Potent inhibitors of NUDT5 silence hormone signaling in breast cancer -

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Basic information

Entry
Database: PDB / ID: 5nwh
TitlePotent inhibitors of NUDT5 silence hormone signaling in breast cancer
ComponentsADP-sugar pyrophosphatase
KeywordsHYDROLASE / NUDIX / Inhibitor
Function / homology
Function and homology information


ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / 8-oxo-GDP phosphatase activity ...ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / 8-oxo-GDP phosphatase activity / D-ribose catabolic process / 8-oxo-dGDP phosphatase activity / Phosphate bond hydrolysis by NUDT proteins / ATP generation from poly-ADP-D-ribose / nucleotide metabolic process / snoRNA binding / nucleotidyltransferase activity / chromatin remodeling / magnesium ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-9CH / ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCarter, M. / Stenmark, P.
CitationJournal: Nat Commun / Year: 2018
Title: Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells.
Authors: Page, B.D.G. / Valerie, N.C.K. / Wright, R.H.G. / Wallner, O. / Isaksson, R. / Carter, M. / Rudd, S.G. / Loseva, O. / Jemth, A.S. / Almlof, I. / Font-Mateu, J. / Llona-Minguez, S. / ...Authors: Page, B.D.G. / Valerie, N.C.K. / Wright, R.H.G. / Wallner, O. / Isaksson, R. / Carter, M. / Rudd, S.G. / Loseva, O. / Jemth, A.S. / Almlof, I. / Font-Mateu, J. / Llona-Minguez, S. / Baranczewski, P. / Jeppsson, F. / Homan, E. / Almqvist, H. / Axelsson, H. / Regmi, S. / Gustavsson, A.L. / Lundback, T. / Scobie, M. / Stromberg, K. / Stenmark, P. / Beato, M. / Helleday, T.
History
DepositionMay 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6944
Polymers48,7112
Non-polymers9832
Water82946
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-46 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.561, 40.146, 104.064
Angle α, β, γ (deg.)90.00, 113.38, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein ADP-sugar pyrophosphatase / 8-oxo-dGDP phosphatase / Nuclear ATP-synthesis protein NUDIX5 / Nucleoside diphosphate-linked ...8-oxo-dGDP phosphatase / Nuclear ATP-synthesis protein NUDIX5 / Nucleoside diphosphate-linked moiety X motif 5 / hNUDT5 / YSA1H


Mass: 24355.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT5, NUDIX5, HSPC115 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UKK9, ADP-ribose diphosphatase, 8-oxo-dGDP phosphatase, ADP-D-ribose pyrophosphorylase
#2: Chemical ChemComp-9CH / 7-[[5-(3,4-dichlorophenyl)-1,3,4-oxadiazol-2-yl]methyl]-1,3-dimethyl-8-piperazin-1-yl-purine-2,6-dione


Mass: 491.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20Cl2N8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 37.85 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 26 mg/ml in 0.1 M HEPES, pH 7.5, 300 mM NaCl, 10% Glycerol, and 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.6→46.2 Å / Num. obs: 11883 / % possible obs: 98 % / Redundancy: 3.5 % / Net I/σ(I): 15.6

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Processing

Software
NameVersionClassification
PHENIXdev_1631refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AC9

3ac9


Resolution: 2.6→46.153 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 710 5.97 %
Rwork0.1868 --
obs0.1906 11883 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→46.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 66 46 3135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073171
X-RAY DIFFRACTIONf_angle_d1.3084321
X-RAY DIFFRACTIONf_dihedral_angle_d15.9321193
X-RAY DIFFRACTIONf_chiral_restr0.048484
X-RAY DIFFRACTIONf_plane_restr0.006555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80070.3531540.25072176X-RAY DIFFRACTION98
2.8007-3.08250.30121420.23892202X-RAY DIFFRACTION98
3.0825-3.52840.2741070.21292248X-RAY DIFFRACTION99
3.5284-4.44490.24111690.16772224X-RAY DIFFRACTION99
4.4449-46.16040.21541380.16032323X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 8.994 Å / Origin y: -16.4249 Å / Origin z: -26.9251 Å
111213212223313233
T0.1863 Å2-0.063 Å20.0207 Å2-0.1326 Å2-0.0176 Å2--0.1696 Å2
L1.2025 °2-0.0429 °2-0.1663 °2-0.5545 °20.101 °2--0.9405 °2
S0.069 Å °-0.1336 Å °0.0125 Å °0.1186 Å °-0.0608 Å °0.0945 Å °0.0174 Å °0.0273 Å °0.0003 Å °
Refinement TLS groupSelection details: all

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