3C5U

P38 ALPHA map kinase complexed with a benzothiazole based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3C5U/pdb

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


• Deposited: 2008-02-01 Released: 2008-03-25 
• Deposition Author(s): Sack, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.296 
• R-Value Work: 0.261 
• R-Value Observed: 0.263 

Literature

Benzothiazole based inhibitors of p38alpha MAP kinase.

Liu, C., Lin, J., Pitt, S., Zhang, R.F., Sack, J.S., Kiefer, S.E., Kish, K., Doweyko, A.M., Zhang, H., Marathe, P.H., Trzaskos, J., Mckinnon, M., Dodd, J.H., Barrish, J.C., Schieven, G.L., Leftheris, K.

(2008) Bioorg Med Chem Lett 18: 1874-1879

• PubMed: 18296051 
• DOI: https://doi.org/10.1016/j.bmcl.2008.02.011
• Primary Citation of Related Structures:  
  3C5U


• PubMed Abstract: 
  

  Rational design, synthesis, and SAR studies of a novel class of benzothiazole based inhibitors of p38alpha MAP kinase are described. The issue of metabolic instability associated with vicinal phenyl, benzo[d]thiazol-6-yl oxazoles/imidazoles was addressed by the replacement of the central oxazole or imidazole ring with an aminopyrazole system. The proposed binding mode of this new class of p38alpha inhibitors was confirmed by X-ray crystallographic studies of a representative inhibitor (6a) bound to the p38alpha enzyme.

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Organizational Affiliation: 

Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 42.81 kDa 
• Atom Count: 2,854 
• Modelled Residue Count: 338 
• 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  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P41	B [auth A], C [auth A]	6-[4-(2-fluorophenyl)-1,3-oxazol-5-yl]-N-(1-methylethyl)-1,3-benzothiazol-2-amine C19 H16 F N3 O S FQYJTHIYAQQJAB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P41	BindingDB:  3C5U	IC50: min: 6.4, max: 6.5 (nM) from 2 assay(s)
	PDBBind:  3C5U	IC50: 6.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.296 
• R-Value Work: 0.261 
• R-Value Observed: 0.263 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.4	α = 90
b = 80.4	β = 90
c = 225.323	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
BUSTER-TNT	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Sack, J.S.

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations