3DS6

P38 complex with a phthalazine inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.228 

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Literature

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: 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 ...

    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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A, B, C, D366Homo sapiensMutation(s): 0 
Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A17
Query on A17
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]		N-cyclopropyl-4-methyl-3-[1-(2-methylphenyl)phthalazin-6-yl]benzamide
C26 H23 N3 O
GQXMJOSCBRZMKE-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
A17 BindingDB:  3DS6 Ki: 0.4 (nM) from 1 assay(s)
IC50: 0.8 (nM) from 1 assay(s)
PDBBind:  3DS6 IC50: 0.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.95α = 90
b = 87.884β = 90
c = 224.939γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance