3E93

Crystal Structure of P38 Kinase in Complex with A Biaryl Amide Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3E93/pdb

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


• Deposited: 2008-08-21 Released: 2008-09-30 
• Deposition Author(s): Somers, D.O., Patel, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Kinase array design, back to front: Biaryl amides

Baldwin, I., Bamborough, P., Haslam, C.G., Hunjan, S.S., Longstaff, T., Mooney, C.J., Patel, S., Quinn, J., Somers, D.O.

(2008) Bioorg Med Chem Lett 18: 5285-5289

• PubMed: 18789685 
• DOI: https://doi.org/10.1016/j.bmcl.2008.08.051
• Primary Citation of Related Structures:  
  3E92, 3E93


• PubMed Abstract: 
  

  New kinase inhibitors can be found by synthesis of targeted arrays of compounds designed using system-based knowledge as well as through screening focused or diverse compounds. Most array strategies aim to add functionality to a fragment that binds in the purine subpocket of the ATP-site. Here, an alternative pharmacophore-guided array approach is described which set out to discover novel purine subpocket-binding groups. Results are shown for p38alpha and cFMS kinase, for which multiple distinct series with nanomolar potency were discovered. Some of the compounds showed potency in cell-based assays and good pharmacokinetic properties.

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Organizational Affiliation: 

GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK.

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: 43.44 kDa 
• Atom Count: 3,306 
• Modelled Residue Count: 347 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	371	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
19B	B [auth A]	4-methyl-N-(3-morpholin-4-ylphenyl)-3-(3-piperidin-4-yl-1,2-benzisoxazol-6-yl)benzamide C30 H32 N4 O3 UVUGBBNUQBSROH-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
19B	BindingDB:  3E93	Ki: 1.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.768	α = 90
b = 86.044	β = 90
c = 126.285	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-30 
Deposition Author(s): Somers, D.O., Patel, S.

Revision History  

• Version 1.0: 2008-09-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-16
  Changes: Structure summary