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- PDB-9gzv: Crystal structure of human NUDT14 in complex with a potent inhibi... -

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Basic information

Entry
Database: PDB / ID: 9gzv
TitleCrystal structure of human NUDT14 in complex with a potent inhibitor (MA-955-9)
ComponentsUridine diphosphate glucose pyrophosphatase NUDT14
KeywordsHYDROLASE / ADP-sugar pyrophosphatase / Dimer
Function / homology
Function and homology information


Synthesis of dolichyl-phosphate-glucose / UDP-sugar diphosphatase / UDP-sugar diphosphatase activity / ADP-ribose diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / : / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Nucleoside diphosphate pyrophosphatase / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
: / ACETIC ACID / DI(HYDROXYETHYL)ETHER / Uridine diphosphate glucose pyrophosphatase NUDT14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBalikci, E. / Feyerherm, C. / Bradshaw, W. / Apostolidou, M. / Adcock, C. / McGown, A. / Spencer, J. / Huber, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)875510European Union
CitationJournal: To Be Published
Title: Crystal structure of human NUDT14 in complex with an inhibitor (MA-955-9)
Authors: Balikci, E. / Feyerherm, C. / Bradshaw, W. / Apostolidou, M. / Adcock, C. / McGown, A. / Spencer, J. / Huber, K.
History
DepositionOct 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine diphosphate glucose pyrophosphatase NUDT14
B: Uridine diphosphate glucose pyrophosphatase NUDT14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,44715
Polymers48,4572
Non-polymers1,99113
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10500 Å2
ΔGint-40 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.989, 98.578, 168.783
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21B-451-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uridine diphosphate glucose pyrophosphatase NUDT14 / UDPG pyrophosphatase / UGPPase / Nucleoside diphosphate-linked moiety X motif 14 / Nudix motif 14


Mass: 24228.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT14, UGPP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O95848, UDP-sugar diphosphatase

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Non-polymers , 7 types, 183 molecules

#2: Chemical ChemComp-A1IRF / 1-(1-methylpiperidin-4-yl)-3-(3-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 400.476 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H24N6O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16% PEG8000, 20% Glycerol, 0.16M Calcium Acetate, 0.1M Cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→59.01 Å / Num. obs: 38254 / % possible obs: 98.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 40.78 Å2 / CC1/2: 0.999 / Net I/σ(I): 0.479
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 1624 / CC1/2: 0.406

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→59.01 Å / SU ML: 0.2896 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9738
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2352 1851 4.88 %
Rwork0.2006 36091 -
obs0.2023 37942 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.37 Å2
Refinement stepCycle: LAST / Resolution: 1.95→59.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 138 170 3645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723566
X-RAY DIFFRACTIONf_angle_d0.93354840
X-RAY DIFFRACTIONf_chiral_restr0.0529516
X-RAY DIFFRACTIONf_plane_restr0.0098627
X-RAY DIFFRACTIONf_dihedral_angle_d19.69691291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.4396950.37662237X-RAY DIFFRACTION79.86
2-2.060.33951340.31622630X-RAY DIFFRACTION93.69
2.06-2.130.32991310.29512809X-RAY DIFFRACTION99.73
2.13-2.20.33721440.26932774X-RAY DIFFRACTION99.86
2.2-2.290.28821440.23552821X-RAY DIFFRACTION99.93
2.29-2.40.22371400.21422802X-RAY DIFFRACTION99.9
2.4-2.520.23091540.21792806X-RAY DIFFRACTION99.93
2.52-2.680.27991560.23142801X-RAY DIFFRACTION100
2.68-2.890.25931430.23762833X-RAY DIFFRACTION100
2.89-3.180.26691460.22022844X-RAY DIFFRACTION100
3.18-3.640.21321750.19082821X-RAY DIFFRACTION100
3.64-4.580.20671410.16022890X-RAY DIFFRACTION100
4.58-59.010.19561480.16663023X-RAY DIFFRACTION99.97

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