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- PDB-9i6e: Crystal structure of DNPH1 bound by compound 5. -

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Basic information

Entry
Database: PDB / ID: 9i6e
TitleCrystal structure of DNPH1 bound by compound 5.
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
: / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.489 Å
AuthorsCollie, G.W.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery and Optimization of a Non-Nucleoside-Based Series of Inhibitors of 2'-Deoxynucleoside 5'-Monophosphate Glycosidase (DNPH1).
Authors: Barlaam, B. / Alonso-Crisostomo, L. / Anderson, N.A. / Argyrou, A. / Astles, P.C. / Cadogan, E.B. / Carlino, L. / Collie, G.W. / Davies, N.L. / Hall, J. / Kitching, L. / Li, X. / ...Authors: Barlaam, B. / Alonso-Crisostomo, L. / Anderson, N.A. / Argyrou, A. / Astles, P.C. / Cadogan, E.B. / Carlino, L. / Collie, G.W. / Davies, N.L. / Hall, J. / Kitching, L. / Li, X. / Michopoulos, F. / Milbradt, A.G. / Nikkila, J. / Northall, S. / O'Connor, M.J. / Pei, X. / Shaw, J. / Slade, D. / Southgate, H. / Stead, D. / Stubbs, C.J. / Whitehurst, B.C. / Xing, B. / Yuan, Y. / Zhou, J.
History
DepositionJan 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0674
Polymers34,3492
Non-polymers7192
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-31 kcal/mol
Surface area12160 Å2
Unit cell
Length a, b, c (Å)36.095, 41.391, 45.815
Angle α, β, γ (deg.)90.12, 108.08, 106.17
Int Tables number1
Space group name H-MP1

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Components

#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.: 2
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
#2: Chemical ChemComp-A1I0K / 4-[[1,1-bis(oxidanylidene)-7-propan-2-yl-4~{H}-1$l^{6},2,4-benzothiadiazin-3-yl]amino]benzoic acid


Mass: 359.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 1.81 Å3/Da / Density % sol: 32.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 8 % PEG3350, 0.1 M PCTP buffer pH 4.5

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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: Dec 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.489→39.567 Å / Num. obs: 27487 / % possible obs: 80.8 % / Redundancy: 1.8 % / CC1/2: 0.999 / Net I/σ(I): 7.7
Reflection shellResolution: 1.489→1.624 Å / Num. unique obs: 1375 / CC1/2: 0.864

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.489→17.72 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 1403 -RANDOM
Rwork0.2109 ---
obs0.2121 27469 69.6 %-
Displacement parametersBiso mean: 18.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.5046 Å2-0.4595 Å20.4664 Å2
2--0.2298 Å2-0.1073 Å2
3---0.2748 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.489→17.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 50 153 2290
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112183HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.022963HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d742SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes381HARMONIC5
X-RAY DIFFRACTIONt_it2183HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion265SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2093SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion17.22
LS refinement shellResolution: 1.49→1.57 Å
RfactorNum. reflection% reflection
Rfree0.3181 26 -
Rwork0.2584 --
obs0.2611 550 9.36 %

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