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

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Basic information

Entry
Database: PDB / ID: 9hbm
TitleCrystal structure of human NUDT14 in complex with a potent inhibitor (MA-955-10)
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 / protein N-linked glycosylation via asparagine / 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
: / Uridine diphosphate glucose pyrophosphatase NUDT14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsBalikci, E. / Feyerherm, C. / 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 a potent inhibitor (MA-955-10)
Authors: Balikci, E. / Feyerherm, C. / Apostolidou, M. / Adcock, C. / McGown, A. / Spencer, J. / Huber, K.
History
DepositionNov 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 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)49,2386
Polymers48,4572
Non-polymers7824
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-57 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.420, 71.150, 111.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#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
#2: Chemical ChemComp-A1ITN / 1-(1-methylpiperidin-4-yl)-3-(4-propan-2-yloxyphenyl)pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 366.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium Chloride, 25% PEG3350, 0.1M Bis-Tris ph 5.5

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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: 1.83→52.39 Å / Num. obs: 46786 / % possible obs: 96.08 % / Redundancy: 10.5 % / Biso Wilson estimate: 40.67 Å2 / CC1/2: 0.999 / Net I/σ(I): 7.84
Reflection shellResolution: 1.83→1.86 Å / Num. unique obs: 41220 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→52.39 Å / SU ML: 0.3417 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.9221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2694 1951 4.8 %
Rwork0.2442 38659 -
obs0.2454 40610 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.93 Å2
Refinement stepCycle: LAST / Resolution: 1.83→52.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 56 156 3564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263536
X-RAY DIFFRACTIONf_angle_d0.60284819
X-RAY DIFFRACTIONf_chiral_restr0.0394524
X-RAY DIFFRACTIONf_plane_restr0.0053625
X-RAY DIFFRACTIONf_dihedral_angle_d15.65031328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.880.45921130.53621906X-RAY DIFFRACTION68.09
1.88-1.930.55041310.43552408X-RAY DIFFRACTION85.09
1.93-1.980.41631330.38742690X-RAY DIFFRACTION94.32
1.98-2.050.3961420.34372770X-RAY DIFFRACTION98.54
2.05-2.120.34381300.31652829X-RAY DIFFRACTION99.46
2.12-2.210.36091400.30682839X-RAY DIFFRACTION99.73
2.21-2.310.37611320.29452857X-RAY DIFFRACTION99.83
2.31-2.430.33821650.28562819X-RAY DIFFRACTION99.63
2.43-2.580.28741330.27532901X-RAY DIFFRACTION99.9
2.58-2.780.28661420.27192845X-RAY DIFFRACTION99.83
2.78-3.060.3571550.27422871X-RAY DIFFRACTION99.9
3.06-3.50.2531180.2442931X-RAY DIFFRACTION100
3.5-4.410.22031400.20542947X-RAY DIFFRACTION99.97
4.41-52.390.20591770.19543046X-RAY DIFFRACTION99.91

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