5EKN

Crystal structure of MAPK13 complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

First comprehensive structural and biophysical analysis of MAPK13 inhibitors targeting DFG-in and DFG-out binding modes.

Yurtsever, Z.Patel, D.A.Kober, D.L.Su, A.Miller, C.A.Romero, A.G.Holtzman, M.J.Brett, T.J.

(2016) Biochim Biophys Acta 1860: 2335-2344

  • DOI: 10.1016/j.bbagen.2016.06.023
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • P38 MAP kinases are centrally involved in mediating extracellular signaling in various diseases. While much attention has previously been focused on the ubiquitously expressed family member MAPK14 (p38α), recent studies indicate that family members s ...

    P38 MAP kinases are centrally involved in mediating extracellular signaling in various diseases. While much attention has previously been focused on the ubiquitously expressed family member MAPK14 (p38α), recent studies indicate that family members such as MAPK13 (p38δ) display a more selective cellular and tissue expression and might therefore represent a specific kinase to target in certain diseases.


    Organizational Affiliation

    Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States; Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110, United States; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, United States; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States. Electronic address: tbrett@wustl.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 13
A
371Homo sapiensMutation(s): 0 
Gene Names: MAPK13PRKM13SAPK4
EC: 2.7.11.24
Find proteins for O15264 (Homo sapiens)
Go to UniProtKB:  O15264
NIH Common Fund Data Resources
PHAROS  O15264
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N58
Query on N58

Download CCD File 
A
1-(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)-3-[4-(pyridin-4-ylsulfanyl)phenyl]urea
C20 H23 N5 O S
FDHKHZIFBOZGKU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
  • Diffraction Data DOI: 10.15785/SBGRID/341 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.047α = 90
b = 70.206β = 90
c = 92.908γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01-HL119813

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references
  • Version 1.2: 2016-09-14
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.5: 2019-12-04
    Changes: Author supporting evidence