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- PDB-9feg: PARP15 in complex with a quinazolin-4-one inhibitor -

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Basic information

Entry
Database: PDB / ID: 9feg
TitlePARP15 in complex with a quinazolin-4-one inhibitor
ComponentsProtein mono-ADP-ribosyltransferase PARP15
KeywordsTRANSFERASE / Inhibitor / PARP15 / ARTD7
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: 1.75 Å
AuthorsBosetti, C. / Lehtio, L.
Funding support Finland, 1items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation Finland
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Substitutions at the C-8 position of quinazolin-4-ones improve the potency of nicotinamide site binding tankyrase inhibitors.
Authors: Bosetti, C. / Kampasis, D. / Brinch, S.A. / Galera-Prat, A. / Karelou, M. / Dhakar, S.S. / Alaviuhkola, J. / Waaler, J. / Lehtio, L. / Kostakis, I.K.
History
DepositionMay 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protein mono-ADP-ribosyltransferase PARP15
A: Protein mono-ADP-ribosyltransferase PARP15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5135
Polymers45,9362
Non-polymers5783
Water3,855214
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-21 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.263, 68.460, 159.596
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 (E. coli)
References: UniProt: Q460N3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-A1H44 / (2~{R})-~{N}-[2-(4-~{tert}-butylphenyl)-4-oxidanylidene-3~{H}-quinazolin-8-yl]-2,3-bis(oxidanyl)propanamide


Mass: 381.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: Growth solution: 200 mM NH4Cl, 20 % PEG3350 Cryo solution: 200 mM NH4Cl, 30 % MPD.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 50967 / % possible obs: 100 % / Redundancy: 6.53 % / Biso Wilson estimate: 19.54 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.51
Reflection shellResolution: 1.75→1.86 Å / Num. unique obs: 8073 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→43.55 Å / SU ML: 0.2212 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2127 2548 5 %
Rwork0.182 48415 -
obs0.1836 50963 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 40 214 3416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01043364
X-RAY DIFFRACTIONf_angle_d0.8474578
X-RAY DIFFRACTIONf_chiral_restr0.0554479
X-RAY DIFFRACTIONf_plane_restr0.009598
X-RAY DIFFRACTIONf_dihedral_angle_d12.59931235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.28111360.27332605X-RAY DIFFRACTION99.78
1.78-1.820.31481410.25732670X-RAY DIFFRACTION100
1.82-1.860.251390.24472642X-RAY DIFFRACTION100
1.86-1.90.28311410.22392672X-RAY DIFFRACTION99.96
1.9-1.950.26131390.21222648X-RAY DIFFRACTION99.96
1.95-20.23541390.19572641X-RAY DIFFRACTION100
2-2.060.22911420.19732691X-RAY DIFFRACTION99.96
2.06-2.130.22211380.19822630X-RAY DIFFRACTION99.96
2.13-2.20.2671400.19262668X-RAY DIFFRACTION100
2.2-2.290.20461410.17672676X-RAY DIFFRACTION99.96
2.29-2.40.21521410.18262663X-RAY DIFFRACTION99.93
2.4-2.520.18761420.17732710X-RAY DIFFRACTION100
2.52-2.680.2341410.17872682X-RAY DIFFRACTION100
2.68-2.890.21521420.17742693X-RAY DIFFRACTION100
2.89-3.180.21641430.18262710X-RAY DIFFRACTION100
3.18-3.640.21371440.17272737X-RAY DIFFRACTION99.97
3.64-4.580.15381460.14562782X-RAY DIFFRACTION99.97
4.58-43.550.19371530.17282895X-RAY DIFFRACTION99.74

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