Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 43.00 kDa 
• Atom Count: 3013 
• Modelled Residue Count: 341 
• Deposited Residue Count: 371 
• Unique protein chains: 1

5EKO

Crystal structure of MAPK13 complex with inhibitor

• PDB DOI: 10.2210/pdb5EKO/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-03 Released: 2016-07-06 
• Deposition Author(s): Brett, T.J., Miller, C.A., Yurtsever, Z.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.241 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

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

• PubMed: 27369736 
• DOI: 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.

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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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 13	A	371	Homo sapiens	Mutation(s): 0  Gene Names: MAPK13, PRKM13, SAPK4 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for O15264 (Homo sapiens) Explore O15264  Go to UniProtKB:  O15264
PHAROS:  O15264

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N17	B [auth A]	3-(4-methyl-1H-imidazol-1-yl)-N-[4-(pyridin-4-yloxy)phenyl]benzamide C22 H18 N4 O2 TXKSFDQJSFSHRB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.241 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data DOI: 10.15785/SBGRID/342 SBGrid

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.263	α = 90
b = 69.669	β = 90
c = 93.068	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-11-03 
• Released Date: 2016-07-06 
Deposition Author(s): Brett, T.J., Miller, C.A., Yurtsever, Z.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01-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