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- PDB-9rlo: PARP15 catalytic domain in complex with OUL250 -

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Basic information

Entry
Database: PDB / ID: 9rlo
TitlePARP15 catalytic domain in complex with OUL250
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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / 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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / 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: 1.9 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)46,6085
Polymers45,9362
Non-polymers6733
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.400, 68.880, 160.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-A1JG9 / 4-[[1,4-bis(oxidanylidene)-2,3-dihydrophthalazin-6-yl]oxy]benzamide


Mass: 297.266 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11N3O4 / 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.: 202 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
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: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 40283 / % possible obs: 99 % / Redundancy: 4.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.106 / Net I/σ(I): 9.41
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.33 % / Rmerge(I) obs: 0.628 / Num. unique obs: 2922 / CC1/2: 0.684 / Rrim(I) all: 0.719 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.732 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.129 / SU ML: 0.112 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.129
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2204 2015 5.002 %
Rwork0.1817 38268 -
all0.184 --
obs-40283 98.958 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.314 Å2
Baniso -1Baniso -2Baniso -3
1--1.953 Å2-0 Å2-0 Å2
2---0.857 Å20 Å2
3---2.81 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 48 202 3445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133351
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153028
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.6624548
X-RAY DIFFRACTIONr_angle_other_deg1.3481.5896962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9955395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79722.5192
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.809102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3815542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6831520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
X-RAY DIFFRACTIONr_nbd_refined0.2090.2560
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.22711
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21594
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21602
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2193
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0350.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.210
X-RAY DIFFRACTIONr_nbd_other0.1350.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.217
X-RAY DIFFRACTIONr_mcbond_it2.82.8221577
X-RAY DIFFRACTIONr_mcbond_other2.7972.8211576
X-RAY DIFFRACTIONr_mcangle_it4.2854.2161967
X-RAY DIFFRACTIONr_mcangle_other4.2854.2181968
X-RAY DIFFRACTIONr_scbond_it3.5583.2951774
X-RAY DIFFRACTIONr_scbond_other3.5573.2971775
X-RAY DIFFRACTIONr_scangle_it5.4254.7792579
X-RAY DIFFRACTIONr_scangle_other5.4234.7822580
X-RAY DIFFRACTIONr_lrange_it7.77633.6073721
X-RAY DIFFRACTIONr_lrange_other7.74533.4563692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.311470.2952777X-RAY DIFFRACTION99.4558
1.949-2.0030.3381430.2652729X-RAY DIFFRACTION99.6876
2.003-2.0610.2321420.2422700X-RAY DIFFRACTION99.6843
2.061-2.1240.2781350.2432549X-RAY DIFFRACTION99.4811
2.124-2.1940.2831320.2132508X-RAY DIFFRACTION99.6979
2.194-2.2710.2331280.2032444X-RAY DIFFRACTION99.0755
2.271-2.3560.2551230.1922339X-RAY DIFFRACTION99.5552
2.356-2.4530.2281190.1892248X-RAY DIFFRACTION99.412
2.453-2.5620.2531130.1872157X-RAY DIFFRACTION98.9538
2.562-2.6870.2281090.1782063X-RAY DIFFRACTION97.9702
2.687-2.8320.2271040.1591988X-RAY DIFFRACTION99.4769
2.832-3.0040.234990.1771882X-RAY DIFFRACTION99.348
3.004-3.2110.237930.1781760X-RAY DIFFRACTION99.0909
3.211-3.4680.208880.1761666X-RAY DIFFRACTION98.8726
3.468-3.7990.2800.1561527X-RAY DIFFRACTION98.6495
3.799-4.2470.172710.1431356X-RAY DIFFRACTION97.7397
4.247-4.9040.152640.1341213X-RAY DIFFRACTION96.0873
4.904-6.0040.173550.1711049X-RAY DIFFRACTION97.6991
6.004-8.4860.211450.156841X-RAY DIFFRACTION98.4444
8.486-43.7320.183250.183472X-RAY DIFFRACTION92.2078

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