5EKO

Crystal structure of MAPK13 complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  

  • 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; Biochemistry Program, 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 13
A
371Homo sapiensMutation(s): 0 
Gene Names: MAPK13 (PRKM13, SAPK4)
EC: 2.7.11.24
Find proteins for O15264 (Homo sapiens)
Go to Gene View: MAPK13
Go to UniProtKB:  O15264
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N17
Query on N17

Download SDF File 
Download CCD File 
A
3-(4-methyl-1H-imidazol-1-yl)-N-[4-(pyridin-4-yloxy)phenyl]benzamide
C22 H18 N4 O2
TXKSFDQJSFSHRB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N17IC50: 10200 - 15785 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 61.263α = 90.00
b = 69.669β = 90.00
c = 93.068γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited StatesR01-HL119813

Revision History 

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