3L8X

P38 alpha kinase complexed with a pyrazolo-pyrimidine based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3L8X/pdb
• Entry: 3L8X supersedes: 3CG2

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


• Deposited: 2010-01-04 Released: 2010-03-02 
• Deposition Author(s): Sack, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.319 
• R-Value Work: 0.225 

Literature

Pyrazolo-Pyrimidines: A Novel Heterocyclic Scaffold for Potent and Selective P38 Alpha Inhibitors.

Das, J., Moquin, R.V., Pitt, S., Zhang, R., Shen, D.R., Mcintyre, K.W., Gillooly, K., Doweyko, A.M., Sack, J.S., Zhang, H., Kiefer, S.E., Kish, K., Mckinnon, M., Barrish, J.C., Dodd, J.H., Schieven, G.L., Leftheris, K.

(2008) Bioorg Med Chem Lett 18: 2652

• PubMed: 18359226 
• DOI: https://doi.org/10.1016/j.bmcl.2008.03.019
• Primary Citation of Related Structures:  
  3L8X


• PubMed Abstract: 
  

  The synthesis and structure-activity relationships (SAR) of p38 alpha MAP kinase inhibitors based on a pyrazolo-pyrimidine scaffold are described. These studies led to the identification of compound 2x as a potent and selective inhibitor of p38 alpha MAP kinase with excellent cellular potency toward the inhibition of TNFalpha production. Compound 2x was highly efficacious in vivo in inhibiting TNFalpha production in an acute murine model of TNFalpha production. X-ray co-crystallography of a pyrazolo-pyrimidine analog 2b bound to unphosphorylated p38 alpha is also disclosed.

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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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 42.46 kDa 
• Atom Count: 2,652 
• Modelled Residue Count: 326 
• 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: CSBP, CSBP1, CSBP2, CSPB1, MAPK14, 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
N4D	B [auth A]	N,4-dimethyl-3-[(1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino]benzamide C20 H18 N6 O OYTBZXSFNNAVKU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
N4D	PDBBind:  3L8X	Kd: 10 (nM) from 1 assay(s)
	BindingDB:  3L8X	IC50: 10 (nM) from 1 assay(s)
	Binding MOAD:  3L8X	IC50: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.319 
• R-Value Work: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.392	α = 90
b = 71.148	β = 90
c = 73.12	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Sack, J.S.
• This entry supersedes: 3CG2

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-09-02
  Changes: Derived calculations, Structure summary
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references