3QUE

Human p38 MAP Kinase in Complex with Skepinone-L

• PDB DOI: https://doi.org/10.2210/pdb3QUE/pdb

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


• Deposited: 2011-02-23 Released: 2012-01-18 
• Deposition Author(s): Gruetter, C., Mayer-Wrangowski, S., Richters, A., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.311 
• R-Value Work: 0.223 
• R-Value Observed: 0.230 

Starting Model: experimental

Literature

Skepinone-L is a selective p38 mitogen-activated protein kinase inhibitor.

Koeberle, S.C., Romir, J., Fischer, S., Koeberle, A., Schattel, V., Albrecht, W., Grutter, C., Werz, O., Rauh, D., Stehle, T., Laufer, S.A.

(2012) Nat Chem Biol 8: 141-143

• PubMed: 22198732 
• DOI: https://doi.org/10.1038/nchembio.761
• Primary Citation of Related Structures:  
  3QUE, 3ZYA


• PubMed Abstract: 
  

  Until now, a lack of inhibitors with high potency and selectivity in vivo has hampered investigation of the p38 mitogen-activated protein kinase (MAPK) signaling pathway. We describe the design of skepinone-L, which is, to our knowledge, the first ATP-competitive p38 MAPK inhibitor with excellent in vivo efficacy and selectivity. Therefore, skepinone-L is a valuable probe for chemical biology research, and it may foster the development of a unique class of kinase inhibitors.

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Organizational Affiliation: 

Institute of Pharmacy, University of Tübingen, Tübingen, Germany.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 42.28 kDa 
• Atom Count: 2,849 
• Modelled Residue Count: 343 
• 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 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 GTEx:  ENSG00000112062

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3FF	D [auth A]	2-[(2,4-difluorophenyl)amino]-7-{[(2R)-2,3-dihydroxypropyl]oxy}-10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-one C24 H21 F2 N O4 HXMGCTFLLWPVFM-GOSISDBHSA-N
BOG	B [auth A], C [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3FF	PDBBind:  3QUE	Kd: 1.5 (nM) from 1 assay(s)
	BindingDB:  3QUE	IC50: min: 5, max: 40 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.311 
• R-Value Work: 0.223 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.408	α = 90
b = 74.016	β = 90
c = 77.47	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Gruetter, C., Mayer-Wrangowski, S., Richters, A., Rauh, D.

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary