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- PDB-9i9q: Crystal structure of DNPH1 bound by compound 2. -

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Basic information

Entry
Database: PDB / ID: 9i9q
TitleCrystal structure of DNPH1 bound by compound 2.
Components5-hydroxymethyl-dUMP N-hydrolase
KeywordsHYDROLASE / DNPH1 / inhibitor / small molecule / drug discovery / DDR / DNA damage response
Function / homology
Function and homology information


purine nucleotide catabolic process / deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / dGMP catabolic process / Purine catabolism / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth ...purine nucleotide catabolic process / deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / dGMP catabolic process / Purine catabolism / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
2-deoxynucleoside 5-phosphate N-hydrolase 1, DNPH1 / : / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase
Similarity search - Domain/homology
: / ETHANOL / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.721 Å
AuthorsCollie, G.W.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2025
Title: Use of Direct-to-Biology Strategies for the Discovery of 2'-Deoxynucleoside 5'-Monophosphate N-Glycosidase (DNPH1) PROTACs.
Authors: Anderson, N.A. / Barlaam, B. / Argyrou, A. / Astles, P.C. / Bruss, H. / Cadogan, E.B. / Carlino, L. / Alonso-Crisostomo, L. / Collie, G.W. / Edwards, A.J. / Gryniukova, A. / Hall, J. / ...Authors: Anderson, N.A. / Barlaam, B. / Argyrou, A. / Astles, P.C. / Bruss, H. / Cadogan, E.B. / Carlino, L. / Alonso-Crisostomo, L. / Collie, G.W. / Edwards, A.J. / Gryniukova, A. / Hall, J. / Jamal, K. / Kent, J. / Kitching, L. / Kourra, C. / Lam, C. / Milbradt, A.G. / Nikkila, J. / Northall, S. / O'Connor, M.J. / Overman, J. / Pathe, C. / Savory, W. / Slade, D. / Spencer, J.A. / Stead, D. / Stubbs, C.J. / Whitehurst, B.C. / Winfield, S.
History
DepositionFeb 6, 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

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Assembly

Deposited unit
A: 5-hydroxymethyl-dUMP N-hydrolase
B: 5-hydroxymethyl-dUMP N-hydrolase
C: 5-hydroxymethyl-dUMP N-hydrolase
D: 5-hydroxymethyl-dUMP N-hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,80115
Polymers68,6974
Non-polymers2,10411
Water4,486249
1
A: 5-hydroxymethyl-dUMP N-hydrolase
B: 5-hydroxymethyl-dUMP N-hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4378
Polymers34,3492
Non-polymers1,0886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-52 kcal/mol
Surface area11870 Å2
2
C: 5-hydroxymethyl-dUMP N-hydrolase
D: 5-hydroxymethyl-dUMP N-hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3647
Polymers34,3492
Non-polymers1,0155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-64 kcal/mol
Surface area12180 Å2
Unit cell
Length a, b, c (Å)74.887, 74.887, 253.173
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-342-

HOH

21A-380-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
5-hydroxymethyl-dUMP N-hydrolase / 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 / c-Myc-responsive protein RCL


Mass: 17174.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNPH1, C6orf108, RCL / Production host: Escherichia coli (E. coli)
References: UniProt: O43598, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 5 types, 260 molecules

#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-A1I1M / 2-[1-methyl-5-[[1-[2-(methylamino)phenyl]carbonylpiperidin-4-yl]amino]-1,2,4-triazol-3-yl]-1~{H}-indole-6-carbonitrile


Mass: 454.527 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H26N8O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15 % PEG8000, 0.1 M PCTP pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.721→71.811 Å / Num. obs: 55740 / % possible obs: 95.4 % / Redundancy: 15.1 % / CC1/2: 0.998 / Net I/σ(I): 16.9
Reflection shellResolution: 1.721→1.893 Å / Num. unique obs: 2787 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.721→34.23 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.147 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.13
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 2804 -RANDOM
Rwork0.2255 ---
obs0.2262 55725 71.9 %-
Displacement parametersBiso mean: 34.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.2412 Å20 Å20 Å2
2--0.2412 Å20 Å2
3----0.4823 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.721→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 148 249 4391
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094244HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.855740HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1479SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes725HARMONIC5
X-RAY DIFFRACTIONt_it4244HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion502SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3904SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion17.03
LS refinement shellResolution: 1.721→1.81 Å
RfactorNum. reflection% reflection
Rfree0.2823 47 -
Rwork0.2841 --
obs--10.1 %

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