3OCG

P38 Alpha kinase complexed with a 5-amino-pyrazole based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3OCG/pdb

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


• Deposited: 2010-08-10 Released: 2010-11-17 
• Deposition Author(s): Sack, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.270 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Literature

5-Amino-pyrazoles as potent and selective p38α inhibitors

Das, J., Moquin, R.V., Dyckman, A.J., Li, T., Pitt, S., Zhang, R., Shen, D.R., McIntyre, K.W., Gillooly, K., Doweyko, A.M., Newitt, J.A., Sack, J.S., Zhang, H., Kiefer, S.E., Kish, K., McKinnon, M., Barrish, J.C., Dodd, J.H., Schieven, G.L., Leftheris, K.

(2010) Bioorg Med Chem Lett 20: 6886-6889

• PubMed: 21035336 
• DOI: https://doi.org/10.1016/j.bmcl.2010.10.034
• Primary Citation of Related Structures:  
  3OCG


• PubMed Abstract: 
  

  The synthesis and structure-activity relationships (SAR) of p38α MAP kinase inhibitors based on a 5-amino-pyrazole scaffold are described. These studies led to the identification of compound 2j as a potent and selective inhibitor of p38α MAP kinase with excellent cellular potency toward the inhibition of TNFα production. Compound 2j was highly efficacious in vivo in inhibiting TNFα production in an acute murine model of TNFα production. X-ray co-crystallography of a 5-amino-pyrazole analog 2f bound to unphosphorylated p38α is also disclosed.

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Organizational Affiliation: 

Bristol-Myers Squibb Research and Development, 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: 42.51 kDa 
• Atom Count: 2,875 
• Modelled Residue Count: 336 
• 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
OCG	B [auth A]	5-amino-N-[5-(isoxazol-3-ylcarbamoyl)-2-methylphenyl]-1-phenyl-1H-pyrazole-4-carboxamide C21 H18 N6 O3 DMYYPSLMFSEFCK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OCG	BindingDB:  3OCG	IC50: 3 (nM) from 1 assay(s)
	PDBBind:  3OCG	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.270 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.94	α = 90
b = 71.43	β = 90
c = 80.55	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Sack, J.S.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-09-02
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references