Crystal structure of a N-Phenyl-N'-Naphthylurea analog in complex with p38 MAP kinase

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.230 

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This is version 1.2 of the entry. See complete history


Discovery and characterization of the N-phenyl-N'-naphthylurea class of p38 kinase inhibitors.

Cirillo, P.F.Hickey, E.R.Moss, N.Breitfelder, S.Betageri, R.Fadra, T.Gaenzler, F.Gilmore, T.Goldberg, D.R.Kamhi, V.Kirrane, T.Kroe, R.R.Madwed, J.Moriak, M.Netherton, M.Pargellis, C.A.Patel, U.R.Qian, K.C.Sharma, R.Sun, S.Swinamer, A.Torcellini, C.Takahashi, H.Tsang, M.Xiong, Z.

(2009) Bioorg Med Chem Lett 19: 2386-2391

  • DOI: https://doi.org/10.1016/j.bmcl.2009.03.104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    An effort aimed at exploring structural diversity in the N-pyrazole-N'-naphthylurea class of p38 kinase inhibitors led to the synthesis and characterization of N-phenyl-N'-naphthylureas. Examples of these compounds displayed excellent inhibition of TNF-alpha production in vitro, as well as efficacy in a mouse model of lipopolysaccharide induced endotoxemia. In addition, perspective is provided on the role of a sulfonamide functionality in defining inhibitor potency.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Boehringer Ingelheim Pharmaceutical, Inc., 900 Ridgebury Road, Ridgefield, CT 06877, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14360Homo 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 B10

Download Ideal Coordinates CCD File 
B [auth A]N-{5-tert-butyl-2-methoxy-3-[({4-[6-(morpholin-4-ylmethyl)pyridin-3-yl]naphthalen-1-yl}carbamoyl)amino]phenyl}methanesulfonamide
C33 H39 N5 O5 S
Binding Affinity Annotations 
IDSourceBinding Affinity
B10 Binding MOAD:  3GI3 Kd: 1.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.01α = 90
b = 74.14β = 90
c = 74.4γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2009-10-20 
  • Deposition Author(s): Qian, K.C.

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-20
    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