3KF7

Crystal Structure of Human p38alpha Complexed With a Triazolopyrimidine compound

• PDB DOI: https://doi.org/10.2210/pdb3KF7/pdb

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


• Deposited: 2009-10-27 Released: 2009-12-29 
• Deposition Author(s): Shieh, H.-S., Williams, J.M., Stegeman, R.A., Xing, L., Jerome, K.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.274 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

Literature

Continued exploration of the triazolopyridine scaffold as a platform for p38 MAP kinase inhibition.

Jerome, K.D., Rucker, P.V., Xing, L., Shieh, H.S., Baldus, J.E., Selness, S.R., Letavic, M.A., Braganza, J.F., McClure, K.F.

(2010) Bioorg Med Chem Lett 20: 469-473

• PubMed: 19969459 
• DOI: https://doi.org/10.1016/j.bmcl.2009.11.114
• Primary Citation of Related Structures:  
  3KF7


• PubMed Abstract: 
  

  The structure based drug design, synthesis and structure-activity relationship of a series of C6 sulfur linked triazolopyridine based p38 inhibitors are described. The metabolic deficiencies of this series were overcome through changes in the C6 linker from sulfur to methylene, which was predicted by molecular modeling to be bioisosteric. X-ray of the ethylene linked compound 61 confirmed the predicted binding orientation of the scaffold in the p38 enzyme.

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Organizational Affiliation: 

Pfizer Global Research and Development, St. Louis Laboratories, 700 Chesterfield Pkwy. W., Chesterfield, MO 63017, USA. [e-mail]

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: 41.74 kDa 
• Atom Count: 2,890 
• Modelled Residue Count: 337 
• 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: CSBP, CSBP1, CSBP2, CSPB1, MAPK14, MXI2, THP-1 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
L9G	B [auth A]	3-{6-[2-(2,4-difluorophenyl)ethyl][1,2,4]triazolo[4,3-a]pyridin-3-yl}-4-methylbenzamide C22 H18 F2 N4 O IECIDZDLEJWPAN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
L9G	PDBBind:  3KF7	IC50: 40 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.274 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.068	α = 90
b = 74.329	β = 90
c = 77.617	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-29 
Deposition Author(s): Shieh, H.-S., Williams, J.M., Stegeman, R.A., Xing, L., Jerome, K.D.

Revision History  

• Version 1.0: 2009-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations