5TBE

Human p38alpha MAP Kinase in Complex with Dibenzosuberone Compound 2

• PDB DOI:  https://doi.org/10.2210/pdb5TBE/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-12 Released: 2017-04-19 
• Deposition Author(s): Buehrmann, M., Rauh, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.254 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

Optimized Target Residence Time: Type I1/2 Inhibitors for p38 alpha MAP Kinase with Improved Binding Kinetics through Direct Interaction with the R-Spine.

Wentsch, H.K., Walter, N.M., Buhrmann, M., Mayer-Wrangowski, S., Rauh, D., Zaman, G.J.R., Willemsen-Seegers, N., Buijsman, R.C., Henning, M., Dauch, D., Zender, L., Laufer, S.

(2017) Angew Chem Int Ed Engl 56: 5363-5367

• PubMed: 28397331 
• DOI: https://doi.org/10.1002/anie.201701185
• Primary Citation of Related Structures:  
  5TBE, 5TCO


• PubMed Abstract: 
  

Skepinone-L was recently reported to be a p38α MAP kinase inhibitor with high potency and excellent selectivity in vitro and in vivo. However, this class of compounds still act as fully ATP-competitive Type I binders which, furthermore, suffer from short residence times at the enzyme. We herein describe a further development with the first Type I1/2 binders for p38α MAP kinase. Type I1/2 inhibitors interfere with the R-spine, inducing a glycine flip and occupying both hydrophobic regions I and II. This design approach leads to prolonged target residence time, binding to both the active and inactive states of the kinase, excellent selectivity, excellent potency on the enzyme level, and low nanomolar activity in a human whole blood assay. This promising binding mode is proven by X-ray crystallography.

---

Organizational Affiliation: 

Institute of Pharmaceutical Sciences, Pharmaceutical and Medicinal Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.96 kDa 
• Atom Count: 2,706 
• Modelled Residue Count: 332 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
78L	B [auth A]	~{N}-[2,4-bis(fluoranyl)-5-[[9-(2-morpholin-4-ylethylcarbamoyl)-11-oxidanylidene-5,6-dihydrodibenzo[1,2-~{d}:1',2'-~{f}][7]annulen-3-yl]amino]phenyl]thiophene-2-carboxamide C33 H30 F2 N4 O4 S KAMAPKIQUKEGQC-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
78L	Binding MOAD:  5TBE	Kd: 4.4 (nM) from 1 assay(s)
	BindingDB:  5TBE	Kd: min: 2.7, max: 4.4 (nM) from 2 assay(s)
		IC50: min: 1, max: 43 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.254 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.67	α = 90
b = 69.39	β = 90
c = 70.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Buehrmann, M., Rauh, D.

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-05-03
  Changes: Database references