Crystal Structure of Human PRPF4B kinase domain in complex with 4-{5-[(2-Chloro-pyridin-4-ylmethyl)-carbamoyl]-thiophen-2-yl}-benzo[b]thiophene-2-carboxylic acid amine

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 

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This is version 1.3 of the entry. See complete history


Evaluation of Cancer Dependence and Druggability of PRP4 Kinase Using Cellular, Biochemical, and Structural Approaches.

Gao, Q.Mechin, I.Kothari, N.Guo, Z.Deng, G.Haas, K.McManus, J.Hoffmann, D.Wang, A.Wiederschain, D.Rocnik, J.Czechtizky, W.Chen, X.McLean, L.Arlt, H.Harper, D.Liu, F.Majid, T.Patel, V.Lengauer, C.Garcia-Echeverria, C.Zhang, B.Cheng, H.Dorsch, M.Huang, S.M.

(2013) J Biol Chem 288: 30125-30138

  • DOI: https://doi.org/10.1074/jbc.M113.473348
  • Primary Citation of Related Structures:  
    4IAN, 4IFC, 4IIR, 4IJP

  • PubMed Abstract: 

    PRP4 kinase is known for its roles in regulating pre-mRNA splicing and beyond. Therefore, a wider spectrum of PRP4 kinase substrates could be expected. The role of PRP4 kinase in cancer is also yet to be fully elucidated. Attaining specific and potent PRP4 inhibitors would greatly facilitate the study of PRP4 biological function and its validation as a credible cancer target. In this report, we verified the requirement of enzymatic activity of PRP4 in regulating cancer cell growth and identified an array of potential novel substrates through orthogonal proteomics approaches. The ensuing effort in structural biology unveiled for the first time unique features of PRP4 kinase domain and its potential mode of interaction with a low molecular weight inhibitor. These results provide new and important information for further exploration of PRP4 kinase function in cancer.

  • Organizational Affiliation

    From Discovery and Early Development, Sanofi Oncology, Cambridge, Massachusetts 02139 and 94400 Vitry-sur-Seine Cedex, France,. Electronic address: alex.huang@sanofi.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PRP4 homolog
A, B
358Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13523 (Homo sapiens)
Explore Q13523 
Go to UniProtKB:  Q13523
PHAROS:  Q13523
GTEx:  ENSG00000112739 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13523
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
1EH BindingDB:  4IJP IC50: 16 (nM) from 1 assay(s)
Binding MOAD:  4IJP IC50: 16 (nM) from 1 assay(s)
PDBBind:  4IJP IC50: 16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.14α = 102.56
b = 52.54β = 105.25
c = 79.13γ = 92.29
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2013-09-18
    Changes: Database references
  • Version 1.2: 2013-11-06
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description