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- PDB-9rg8: Crystal structure of DNPH1 bound by compound 1. -

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Basic information

Entry
Database: PDB / ID: 9rg8
TitleCrystal structure of DNPH1 bound by compound 1.
Components5-hydroxymethyl-dUMP N-hydrolase
KeywordsHYDROLASE / DNPH1
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: 2.07 Å
AuthorsCollie, G.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionJun 5, 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

Downloads & links

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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)34,8673
Polymers34,3492
Non-polymers5191
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-29 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.394, 52.394, 361.382
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122

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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-A1JFX / 2-[1-methyl-5-[[1-[3-(pyrimidin-2-ylamino)phenyl]carbonylpiperidin-4-yl]amino]-1,2,4-triazol-3-yl]-1~{H}-indole-6-carbonitrile


Mass: 518.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N10O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 % PEG3350, 5 % ethanol, 0.1 M MgCl2, 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: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.07→60.23 Å / Num. obs: 19420 / % possible obs: 100 % / Redundancy: 27.9 % / CC1/2: 0.999 / Net I/σ(I): 11.5
Reflection shellResolution: 2.07→2.11 Å / Num. unique obs: 928 / CC1/2: 0.62

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→20.77 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.223 / SU Rfree Blow DPI: 0.205 / SU Rfree Cruickshank DPI: 0.199
RfactorNum. reflection% reflectionSelection details
Rfree0.2993 881 -RANDOM
Rwork0.2419 ---
obs0.2446 19010 98.8 %-
Displacement parametersBiso mean: 62.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.6619 Å20 Å20 Å2
2--0.6619 Å20 Å2
3----1.3238 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.07→20.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 39 53 1961
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081945HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.892628HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d674SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes331HARMONIC5
X-RAY DIFFRACTIONt_it1945HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion233SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1516SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion17.89
LS refinement shellResolution: 2.07→2.09 Å
RfactorNum. reflection% reflection
Rfree0.6084 19 -
Rwork0.4172 --
obs0.4258 433 88.37 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8969-0.0653-0.83891.36151.75232.5867-0.0012-0.1469-0.137-0.1469-0.1231-0.0559-0.137-0.05590.1243-0.0073-0.0023-0.0469-0.0578-0.0241-0.02813.3973-11.5672-12.5022
21.6033-0.30760.6461.9278-0.08211.1809-0.0688-0.0935-0.1371-0.09350.17890.2439-0.13710.2439-0.1101-0.0137-0.05280.01040.0574-0.0712-0.122525.6986-21.1802-17.127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A20 - 160
2X-RAY DIFFRACTION2{ B|* }B20 - 159

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