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- PDB-9rlq: PARP15 catalytic domain in complex with OUL312 -

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Basic information

Entry
Database: PDB / ID: 9rlq
TitlePARP15 catalytic domain in complex with OUL312
ComponentsProtein mono-ADP-ribosyltransferase PARP15
KeywordsTRANSFERASE / Inhibitor / Complex / ADP-ribosyltransferase
Function / homology
Function and homology information


NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression ...NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
: / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like
Similarity search - Domain/homology
: / Protein mono-ADP-ribosyltransferase PARP15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAlaviuhkola, J. / Maksimainen, M.M. / Lehtio, L.
Funding support Finland, 3items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
Academy of Finland347026 Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Optimization of 2,3-dihydrophthalazine-1,4-dione PARP inhibitor scaffold for nanomolar potency and specificity towards human PARP10.
Authors: Alaviuhkola, J. / Nizi, M.G. / Vagaggini, C. / Sarnari, C. / Lippok, B. / Maksimainen, M.M. / Bosetti, C. / Dhakar, S.S. / Manfroni, G. / Massari, S. / Dreassi, E. / Korn, P. / Tabarrini, O. / Lehtio, L.
History
DepositionJun 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 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: Protein mono-ADP-ribosyltransferase PARP15
B: Protein mono-ADP-ribosyltransferase PARP15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3144
Polymers45,9362
Non-polymers3782
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-6 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.020, 67.980, 155.090
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 Protein mono-ADP-ribosyltransferase PARP15 / ADP-ribosyltransferase diphtheria toxin-like 7 / ARTD7 / B-aggressive lymphoma protein 3 / Poly ...ADP-ribosyltransferase diphtheria toxin-like 7 / ARTD7 / B-aggressive lymphoma protein 3 / Poly [ADP-ribose] polymerase 15 / PARP-15


Mass: 22967.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP15, BAL3 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q460N3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-A1JHB / 6-[2-(2-fluorophenyl)ethoxy]-2,3-dihydrophthalazine-1,4-dione


Mass: 300.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13FN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% (w/v) PEG 3350, 0.2 M ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.8→77.55 Å / Num. obs: 45017 / % possible obs: 99.9 % / Redundancy: 11.8 % / Biso Wilson estimate: 17.64 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.241 / Rrim(I) all: 0.252 / Net I/σ(I): 7.88
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 1.321 / Num. unique obs: 3257 / CC1/2: 0.621 / Rrim(I) all: 1.39

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→77.55 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.427
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2803 2000 4.44 %
Rwork0.2242 43017 -
obs0.2267 45017 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.62 Å2
Refinement stepCycle: LAST / Resolution: 1.8→77.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 26 247 3455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01813316
X-RAY DIFFRACTIONf_angle_d1.47964501
X-RAY DIFFRACTIONf_chiral_restr0.0744470
X-RAY DIFFRACTIONf_plane_restr0.0138588
X-RAY DIFFRACTIONf_dihedral_angle_d14.48781236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.36941390.31183010X-RAY DIFFRACTION99.94
1.85-1.90.35891410.29673020X-RAY DIFFRACTION99.94
1.9-1.950.36011410.27953030X-RAY DIFFRACTION99.91
1.95-2.010.32751400.2563023X-RAY DIFFRACTION99.84
2.01-2.090.30341410.24683034X-RAY DIFFRACTION99.81
2.09-2.170.30041420.2333036X-RAY DIFFRACTION100
2.17-2.270.30031420.22983055X-RAY DIFFRACTION99.91
2.27-2.390.26671410.22893041X-RAY DIFFRACTION100
2.39-2.540.30051420.2333058X-RAY DIFFRACTION99.97
2.54-2.730.31221430.22363069X-RAY DIFFRACTION99.97
2.73-3.010.26731440.22533098X-RAY DIFFRACTION99.94
3.01-3.440.24291440.21273109X-RAY DIFFRACTION99.94
3.44-4.340.25031460.1863137X-RAY DIFFRACTION99.97
4.34-77.550.24941540.20523297X-RAY DIFFRACTION99.91
Refinement TLS params.Method: refined / Origin x: 5.70117981329 Å / Origin y: 0.312899556792 Å / Origin z: -24.1168969128 Å
111213212223313233
T0.106288056051 Å2-0.00984449845421 Å20.00323923382105 Å2-0.10036630293 Å2-0.034171530376 Å2--0.231550652998 Å2
L0.956800358825 °2-0.164721946661 °2-0.286350513784 °2-0.56048663182 °20.317331276319 °2--0.657441705714 °2
S0.0125054486548 Å °-0.117530164936 Å °0.0489324974978 Å °0.0287957078468 Å °-0.0207032962025 Å °-0.0132409039884 Å °-0.0187277207974 Å °-0.0121346056368 Å °0.0107024101243 Å °
Refinement TLS groupSelection details: all

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