5V7W

Crystal structure of human PARP14 bound to 2-{[(1-methylpiperidin-4-yl)methyl]amino}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification of PARP14 inhibitors using novel methods for detecting auto-ribosylation.

Yoneyama-Hirozane, M.Matsumoto, S.I.Toyoda, Y.Saikatendu, K.S.Zama, Y.Yonemori, K.Oonishi, M.Ishii, T.Kawamoto, T.

(2017) Biochem Biophys Res Commun 486: 626-631

  • DOI: https://doi.org/10.1016/j.bbrc.2017.03.052
  • Primary Citation of Related Structures:  
    5V7T, 5V7W

  • PubMed Abstract: 

    Poly(ADP-ribose) polymerases (PARPs) use nicotinamide adenine dinucleotide (NAD + ) as a co-substrate to transfer ADP-ribose when it releases nicotinamide as the metabolized product. Enzymes of the PARP family play key roles in detecting and repairing DNA, modifying chromatin, regulating transcription, controlling energy metabolism, and inducing cell death. PARP14, the original member of the PARP family, has been reported to be associated with the development of inflammatory diseases and various cancer types, making it a potential therapeutic target. In this study, we purified the macrodomain-containing PARP14 enzyme and established an assay for detecting the auto-ribosylation activity of PARP14 using RapidFire high-throughput mass spectrometry and immunoradiometric assay using [ 3 H]NAD + . Subsequently, we performed high-throughput screening using the assays and identified small-molecule hit compounds, which showed NAD + -competitive and PARP14-selective inhibitory activities. Co-crystal structures of PARP14 with certain hit compounds revealed that the inhibitors bind to the NAD + -binding site. Finally, we confirmed that the hit compounds interacted with intracellular PARP14 by a cell-based protein stabilization assay. Thus, we successfully identified primary candidate compounds for further investigation.


  • Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. Electronic address: mariko.hirozane@takeda.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 14
A, B
194Homo sapiensMutation(s): 0 
Gene Names: PARP14BAL2KIAA1268
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q460N5 (Homo sapiens)
Explore Q460N5 
Go to UniProtKB:  Q460N5
PHAROS:  Q460N5
GTEx:  ENSG00000173193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ460N5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
91J
Query on 91J

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-{[(1-methylpiperidin-4-yl)methyl]amino}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one
C17 H24 N4 O S
JXQVQMRDGUVMOA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.049α = 90
b = 144.907β = 90
c = 83.428γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Source and taxonomy