P38 Complexed with a quinazoline inhibitor

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.214 

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Discovery of highly selective and potent p38 inhibitors based on a phthalazine scaffold.

Herberich, B.Cao, G.Q.Chakrabarti, P.P.Falsey, J.R.Pettus, L.Rzasa, R.M.Reed, A.B.Reichelt, A.Sham, K.Thaman, M.Wurz, R.P.Xu, S.Zhang, D.Hsieh, F.Lee, M.R.Syed, R.Li, V.Grosfeld, D.Plant, M.H.Henkle, B.Sherman, L.Middleton, S.Wong, L.M.Tasker, A.S.

(2008) J Med Chem 51: 6271-6279

  • DOI: https://doi.org/10.1021/jm8005417
  • Primary Citation of Related Structures:  
    3DS6, 3DT1

  • PubMed Abstract: 

    Investigations into the structure-activity relationships (SAR) of a series of phthalazine-based inhibitors of p38 are described. These efforts originated from quinazoline 1 and through rational design led to the development of a series of orally bioavailable, potent, and selective inhibitors. Kinase selectivity was achieved by exploiting a collection of interactions with p38alpha including close contact to Ala157, occupation of the hydrophobic gatekeeper pocket, and a residue flip with Gly110. Substitutions on the phthalazine influenced the pharmacokinetic properties, of which compound 16 displayed the most desirable profile. Oral dosing (0.03 mg/kg) of 16 in rats 1 h prior to LPS challenge gave a >50% decrease in TNFalpha production.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Amgen, Inc., Thousand Oaks, California 91320-1799, USA. brad.herberich@amgen.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14383Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
GTEx:  ENSG00000112062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on P40

Download Ideal Coordinates CCD File 
B [auth A]N-cyclopropyl-4-methyl-3-{2-[(2-morpholin-4-ylethyl)amino]quinazolin-6-yl}benzamide
C25 H29 N5 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
P40 PDBBind:  3DT1 IC50: 2.4 (nM) from 1 assay(s)
BindingDB:  3DT1 IC50: min: 0.9, max: 2.4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.664α = 90
b = 86.056β = 90
c = 119.345γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-14
    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