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- PDB-9i3q: Crystal structure of DNPH1 bound by compound 2. -

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Basic information

Entry
Database: PDB / ID: 9i3q
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
: / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.597 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 23, 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)35,1494
Polymers34,3492
Non-polymers8012
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-29 kcal/mol
Surface area11820 Å2
Unit cell
Length a, b, c (Å)36.717, 39.605, 48.52
Angle α, β, γ (deg.)91.96, 99.92, 114.71
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-A1IZR / 4-[[1,1-bis(oxidanylidene)-7-propan-2-yl-4~{H}-1$l^{6},2,4-benzothiadiazin-3-yl]amino]-2,6-bis(chloranyl)phenol


Mass: 400.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15Cl2N3O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.83 Å3/Da / Density % sol: 32.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25 % PEG3350, 0.2 M MgCl2, 0.1 M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.597→47.46 Å / Num. obs: 13312 / % possible obs: 79.9 % / Redundancy: 2.7 % / CC1/2: 0.989 / Net I/σ(I): 3.6
Reflection shellResolution: 1.597→1.887 Å / Num. unique obs: 666 / CC1/2: 0.819

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
SCALAdata scaling
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.597→47.46 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.872 / SU R Cruickshank DPI: 0.282 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.267 / SU Rfree Blow DPI: 0.215 / SU Rfree Cruickshank DPI: 0.222
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 658 -RANDOM
Rwork0.2069 ---
obs0.2097 13312 41.3 %-
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.3193 Å20.9617 Å20.3102 Å2
2---0.432 Å2-0.8637 Å2
3---0.7513 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.597→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 50 73 2060
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012026HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.962750HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d687SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes344HARMONIC5
X-RAY DIFFRACTIONt_it2026HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion244SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1781SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion18.82
LS refinement shellResolution: 1.6→1.82 Å
RfactorNum. reflection% reflection
Rfree0.4178 20 -
Rwork0.2089 --
obs0.2196 416 3.96 %

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