3ZYA | pdb_00003zya

Human p38 MAP Kinase in Complex with 2-amino-phenylamino- dibenzosuberone

• PDB DOI: https://doi.org/10.2210/pdb3ZYA/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-18 Released: 2011-12-28 
• Deposition Author(s): Romir, J., Koeberle, S.C., Laufer, S.A., Stehle, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.209 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

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.

(2011) Nat Chem Biol 8: 141

• PubMed: 22198732 
• DOI: https://doi.org/10.1038/nchembio.761
• Primary Citation 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: 42.31 kDa 
• Atom Count: 3,161 
• Modeled Residue Count: 346 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOGEN-ACTIVATED PROTEIN KINASE 14	A	366	Homo sapiens	Mutation(s): 0  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2A8	B [auth A]	2-AMINO-PHENYLAMINO-DIBENZOSUBERONE C21 H18 N2 O VMANCBCSTYKPPA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2A8	BindingDB:  3ZYA	Kd: 7.6 (nM) from 1 assay(s)
		IC50: min: 50, max: 3800 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.209 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.155	α = 90
b = 51.863	β = 90
c = 167.881	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Romir, J., Koeberle, S.C., Laufer, S.A., Stehle, T.

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2012-02-01
  Changes: Other
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description