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- PDB-9rlr: PARP15 catalytic domain in complex with OUL499 -

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Basic information

Entry
Database: PDB / ID: 9rlr
TitlePARP15 catalytic domain in complex with OUL499
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: 2.6 Å
AuthorsAlaviuhkola, J. / 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)46,3955
Polymers45,9362
Non-polymers4593
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.730, 68.940, 160.010
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-A1JHC / 6-[(3-chlorophenyl)methoxy]-2,3-dihydrophthalazine-1,4-dione


Mass: 302.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 18% (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 6M / Detector: PIXEL / Date: Jan 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 16006 / % possible obs: 98.4 % / Redundancy: 6.2 % / CC1/2: 0.966 / Rmerge(I) obs: 0.297 / Rrim(I) all: 0.325 / Net I/σ(I): 5.68
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.836 / Num. unique obs: 1190 / CC1/2: 0.584 / Rrim(I) all: 0.92 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.008 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.851 / SU B: 12.216 / SU ML: 0.254 / Cross valid method: FREE R-VALUE / ESU R: 0.774 / ESU R Free: 0.339
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2743 801 5.004 %
Rwork0.2312 15205 -
all0.233 --
obs-16006 98.438 %
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: 25.511 Å2
Baniso -1Baniso -2Baniso -3
1--1.884 Å2-0 Å20 Å2
2--1.953 Å2-0 Å2
3----0.069 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 29 47 3271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133325
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153014
X-RAY DIFFRACTIONr_ext_dist_refined_d0.3760.150612
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6594511
X-RAY DIFFRACTIONr_angle_other_deg1.3071.5876936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1275395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26922.632190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38915540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4111519
X-RAY DIFFRACTIONr_chiral_restr0.0650.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023825
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02835
X-RAY DIFFRACTIONr_nbd_refined0.20.2509
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.22543
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21550
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21551
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.272
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2180.212
X-RAY DIFFRACTIONr_nbd_other0.2440.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2640.25
X-RAY DIFFRACTIONr_mcbond_it2.1742.5921577
X-RAY DIFFRACTIONr_mcbond_other2.1682.591576
X-RAY DIFFRACTIONr_mcangle_it3.6663.8731967
X-RAY DIFFRACTIONr_mcangle_other3.6683.8751968
X-RAY DIFFRACTIONr_scbond_it2.2112.8331748
X-RAY DIFFRACTIONr_scbond_other2.212.8341749
X-RAY DIFFRACTIONr_scangle_it3.584.1572542
X-RAY DIFFRACTIONr_scangle_other3.5794.1582543
X-RAY DIFFRACTIONr_lrange_it7.91896.16651215
X-RAY DIFFRACTIONr_lrange_other7.91896.16751215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6670.314600.31130X-RAY DIFFRACTION99.8322
2.667-2.740.33570.2781088X-RAY DIFFRACTION100
2.74-2.820.356550.2611051X-RAY DIFFRACTION100
2.82-2.9070.287550.2581034X-RAY DIFFRACTION99.9083
2.907-3.0020.331530.2591002X-RAY DIFFRACTION100
3.002-3.1070.243500.251965X-RAY DIFFRACTION99.9016
3.107-3.2250.309490.237935X-RAY DIFFRACTION100
3.225-3.3560.348480.252903X-RAY DIFFRACTION99.895
3.356-3.5050.222460.224879X-RAY DIFFRACTION100
3.505-3.6760.345380.286722X-RAY DIFFRACTION88.1671
3.676-3.8750.377360.288673X-RAY DIFFRACTION84.0047
3.875-4.110.283400.211761X-RAY DIFFRACTION99.5031
4.11-4.3940.252370.186708X-RAY DIFFRACTION99.866
4.394-4.7450.195350.182664X-RAY DIFFRACTION99.8571
4.745-5.1980.248330.169627X-RAY DIFFRACTION100
5.198-5.810.219300.183570X-RAY DIFFRACTION100
5.81-6.7080.188260.18500X-RAY DIFFRACTION100
6.708-8.2120.145230.176432X-RAY DIFFRACTION99.7807
8.212-11.5980.215190.191360X-RAY DIFFRACTION100
11.598-44.0080.353110.332201X-RAY DIFFRACTION97.6959

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