1WBT

Identification of novel p38 alpha MAP Kinase inhibitors using fragment-based lead generation.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Identification of Novel P38Alpha Map Kinase Inhibitors Using Fragment-Based Lead Generation.

Gill, A.L.Frederickson, M.Cleasby, A.Woodhead, S.J.Carr, M.G.Woodhead, A.J.Walker, M.T.Congreve, M.S.Devine, L.A.Tisi, D.O'Reilly, M.Seavers, L.C.Davis, D.J.Curry, J.Anthony, R.Padova, A.Murray, C.W.Carr, R.A.Jhoti, H.

(2005) J.Med.Chem. 48: 414

  • DOI: 10.1021/jm049575n
  • Primary Citation of Related Structures:  1WBN, 1WBS, 1WBV, 1WBW, 1W82, 1W83, 1W84

  • PubMed Abstract: 
  • We describe the structure-guided optimization of the molecular fragments 2-amino-3-benzyloxypyridine 1 (IC(50) 1.3 mM) and 3-(2-(4-pyridyl)ethyl)indole 2 (IC(50) 35 microM) identified using X-ray crystallographic screening of p38alpha MAP kinase. Usi ...

    We describe the structure-guided optimization of the molecular fragments 2-amino-3-benzyloxypyridine 1 (IC(50) 1.3 mM) and 3-(2-(4-pyridyl)ethyl)indole 2 (IC(50) 35 microM) identified using X-ray crystallographic screening of p38alpha MAP kinase. Using two separate case studies, the article focuses on the key compounds synthesized, the structure-activity relationships and the binding mode observations made during this optimization process, resulting in two potent lead series that demonstrate significant increases in activity. We describe the process of compound elaboration either through the growing out from fragments into adjacent pockets or through the conjoining of overlapping fragments and demonstrate that we have exploited the mobile conserved activation loop, consisting in part of Asp168-Phe169-Gly170 (DFG), to generate significant improvements in potency and kinase selectivity.


    Organizational Affiliation

    Astex Technology, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom. a.gill@astex-technology.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MITOGEN-ACTIVATED PROTEIN KINASE 14
A
360Homo sapiensGene 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
WBT
Query on WBT

Download SDF File 
Download CCD File 
A
3-FLUORO-5-MORPHOLIN-4-YL-N-[1-(2-PYRIDIN-4-YLETHYL)-1H-INDOL-6-YL]BENZAMIDE
C26 H25 F N4 O2
CPFBZMFUCGHBAP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WBTIC50: 340 nM (100) BINDINGDB
WBTIC50: 340 nM BINDINGMOAD
WBTIC50: 340 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.519α = 90.00
b = 85.602β = 90.00
c = 126.577γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENCORphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Source and taxonomy