4IIR

Crystal Structure of AMPPNP-bound Human PRPF4B kinase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 

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:  
    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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PRP4 homologAB358Homo sapiensMutation(s): 0 
Gene Names: KIAA0536PRP4PRP4HPRP4KPRPF4B
EC: 2.7.11.1
Find proteins for Q13523 (Homo sapiens)
Explore Q13523 
Go to UniProtKB:  Q13523
NIH Common Fund Data Resources
PHAROS  Q13523
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.5α = 105.29
b = 52.5β = 103.05
c = 78.79γ = 93.09
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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