Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 43004.30 
• Atom Count: 2800 
• Residue Count: 371 
• Unique protein chains: 1

5EKO

Crystal structure of MAPK13 complex with inhibitor

• DOI: 10.2210/pdb5EKO/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• 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 

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Experimental Data Snapshot

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

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


• 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; 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
Molecule	Chains	Sequence Length	Organism	Details
Mitogen-activated protein kinase 13	A	371	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
N17	A	3-(4-methyl-1H-imidazol-1-yl)-N-[4-(pyridin-4-yloxy)phenyl]benzamide C22 H18 N4 O2 TXKSFDQJSFSHRB-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
N17	IC50: 10200 - 15785 nM (100) BINDINGDB
N17	IC50: 15785 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.241 
• R-Value Work: 0.200 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data DOI: 
  10.15785/SBGRID/342 SBGrid

Unit Cell:

Length (Å)	Angle (°)
a = 61.263	α = 90.00
b = 69.669	β = 90.00
c = 93.068	γ = 90.00

Software Package:

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

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	United States	R01-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