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- PDB-8he8: Human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8he8 | |||||||||
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Title | Human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor | |||||||||
![]() | Poly [ADP-ribose] polymerase 2 | |||||||||
![]() | TRANSFERASE / PARP-2 / DNA ADP-ribosyltransferase / Inhibitor | |||||||||
Function / homology | ![]() response to oxygen-glucose deprivation / hippocampal neuron apoptotic process / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / poly-ADP-D-ribose modification-dependent protein binding ...response to oxygen-glucose deprivation / hippocampal neuron apoptotic process / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / poly-ADP-D-ribose modification-dependent protein binding / HDR through MMEJ (alt-NHEJ) / DNA repair-dependent chromatin remodeling / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / site of DNA damage / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / POLB-Dependent Long Patch Base Excision Repair / extrinsic apoptotic signaling pathway / nucleosome binding / nucleotidyltransferase activity / DNA Damage Recognition in GG-NER / base-excision repair / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair / damaged DNA binding / DNA repair / DNA damage response / chromatin binding / nucleolus / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, X.Y. / Xu, B.L. / Zhou, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of Quinazoline-2,4(1 H ,3 H )-dione Derivatives Containing a Piperizinone Moiety as Potent PARP-1/2 Inhibitors─Design, Synthesis, In Vivo Antitumor Activity, and X-ray Crystal Structure Analysis. Authors: Zhou, J. / Du, T. / Wang, X. / Yao, H. / Deng, J. / Li, Y. / Chen, X. / Sheng, L. / Ji, M. / Xu, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.9 KB | Display | ![]() |
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PDB format | ![]() | 173.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 40 KB | Display | |
Data in CIF | ![]() | 52.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8he7C ![]() 4tvjS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39811.742 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UGN5, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 25% PEG-3350, 0.1 M Tris-HCl pH 8.3-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→48.26 Å / Num. obs: 19445 / % possible obs: 90 % / Redundancy: 4.7 % / Biso Wilson estimate: 56.6 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.071 / Rrim(I) all: 0.164 / Net I/σ(I): 10.18 |
Reflection shell | Resolution: 3.05→3.159 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.5886 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 2013 / CC1/2: 0.785 / Rpim(I) all: 0.2847 / Rrim(I) all: 0.6574 / % possible all: 92.04 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4TVJ Resolution: 3.05→41.09 Å / SU ML: 0.3284 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.7854 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→41.09 Å
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Refine LS restraints |
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LS refinement shell |
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