Crystal structure of MAPK13 complex with inhibitor

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 

This is version 1.6 of the entry. See complete history


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: https://doi.org/10.1016/j.bbagen.2016.06.023
  • Primary Citation of Related Structures:  
    5EKN, 5EKO

  • 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 such as MAPK13 (p38δ) display a more selective cellular and tissue expression and might therefore represent a specific kinase to target in certain diseases. To facilitate the design of potent and specific inhibitors, we present here the structural, biophysical, and functional characterization of two new MAPK13-inhibitor complexes, as well as the first comprehensive structural, biophysical, and functional analysis of MAPK13 complexes with four different inhibitor compounds of greatly varying potency. These inhibitors display IC50 values either in the nanomolar range or micromolar range (>800-fold range). The nanomolar inhibitors exhibit much longer ligand-enzyme complex half-lives compared to the micromolar inhibitors as measured by biolayer interferometry. Crystal structures of the MAPK13 inhibitor complexes reveal that the nanomolar inhibitors engage MAPK13 in the DFG-out binding mode, while the micromolar inhibitors are in the DFG-in mode. Detailed structural and computational docking analyses suggest that this difference in binding mode engagement is driven by conformational restraints imposed by the chemical structure of the inhibitors, and may be fortified by an additional hydrogen bond to MAPK13 in the nanomolar inhibitors. These studies provide a structural basis for understanding the differences in potency exhibited by these inhibitors. They also provide the groundwork for future studies to improve specificity, potency, pharmacodynamics, and pharmacokinetic properties.

  • 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 13371Homo sapiensMutation(s): 0 
Gene Names: MAPK13PRKM13SAPK4
UniProt & NIH Common Fund Data Resources
Find proteins for O15264 (Homo sapiens)
Explore O15264 
Go to UniProtKB:  O15264
PHAROS:  O15264
GTEx:  ENSG00000156711 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15264
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on N17

Download Ideal Coordinates CCD File 
B [auth A]3-(4-methyl-1H-imidazol-1-yl)-N-[4-(pyridin-4-yloxy)phenyl]benzamide
C22 H18 N4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
N17 BindingDB:  5EKO IC50: min: 1.02e+4, max: 1.58e+4 (nM) from 2 assay(s)
Binding MOAD:  5EKO IC50: 1.58e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.263α = 90
b = 69.669β = 90
c = 93.068γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

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  (Full details and data files)

  • 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
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description