4IIR

Crystal Structure of AMPPNP-bound Human PRPF4B kinase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1074/jbc.M113.473348
  • Primary Citation of Related Structures:  

  • 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 poten ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PRP4 homolog
A, B
358Homo sapiensMutation(s): 0 
Gene Names: PRPF4B (KIAA0536, PRP4, PRP4H, PRP4K)
EC: 2.7.11.1
Find proteins for Q13523 (Homo sapiens)
Go to Gene View: PRPF4B
Go to UniProtKB:  Q13523
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.243 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 52.500α = 105.29
b = 52.500β = 103.05
c = 78.790γ = 93.09
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
BUSTERrefinement
BUSTER-TNTrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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