3GI3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1016/j.bmcl.2009.03.104

  • 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 T ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 14
A
360Homo sapiensMutation(s): 0 
Gene Names: MAPK14 (CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A)
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Go to Gene View: MAPK14
Go to UniProtKB:  Q16539
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B10
Query on B10

Download SDF File 
Download CCD File 
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
KLPFPTSVYVEKOL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B10Kd: <1.8 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.010α = 90.00
b = 74.140β = 90.00
c = 74.400γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-03-05 
  • Released Date: 2009-10-20 
  • Deposition Author(s): Qian, K.C.

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance