2GFS

P38 Kinase Crystal Structure in complex with RO3201195


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of S-[5-Amino-1-(4-fluorophenyl)-1H-pyrazol-4-yl]-[3-(2,3-dihydroxypropoxy)phenyl]-methanone (RO3201195), and Orally Bioavailable and Highly Selective Inhibitor of p38 Map Kinase

Goldstein, D.M.Alfredson, T.A.Bertrand, J.Browner, M.F.Clifford, K.Dalrymple, S.Dunn, J.Freire-Moare, J.Harris, S.F.Labadie, S.S.La Fargue, J.Lapierre, J.M.Larrabee, S.Li, F.Papp, E.McWeeney, D.Ramesha, C.Roberts, R.Rotstein, D.San Pablo, B.Sjogren, E.So, O.Y.Talamas, F.X.Tao, W.Trejo, A.Villasenor, A.Welch, M.Welch, T.Weller, P.Whiteley, P.E.Young, K.Zipfel, S.

(2006) J Med Chem 49: 1562-1575

  • DOI: 10.1021/jm050736c
  • Primary Citation of Related Structures:  
    2GFS

  • PubMed Abstract: 
  • A novel class of highly selective inhibitors of p38 MAP kinase was discovered from high throughput screening. The synthesis and optimization of a series of 5-amino-N-phenyl-1H-pyrazol-4-yl-3-phenylmethanones is described. An X-ray crystal structure of this series bound in the ATP binding pocket of unphosphorylated p38alpha established the presence of a unique hydrogen bond between the exocyclic amine of the inhibitor and threonine 106 which likely contributes to the selectivity for p38 ...

    A novel class of highly selective inhibitors of p38 MAP kinase was discovered from high throughput screening. The synthesis and optimization of a series of 5-amino-N-phenyl-1H-pyrazol-4-yl-3-phenylmethanones is described. An X-ray crystal structure of this series bound in the ATP binding pocket of unphosphorylated p38alpha established the presence of a unique hydrogen bond between the exocyclic amine of the inhibitor and threonine 106 which likely contributes to the selectivity for p38. The crystallographic information was used to optimize the potency and physicochemical properties of the series. The incorporation of the 2,3-dihydroxypropoxy moiety on the pyrazole scaffold resulted in a compound with excellent drug-like properties including high oral bioavailability. These efforts identified 63 (RO3201195) as an orally bioavailable and highly selective inhibitor of p38 which was selected for advancement into Phase I clinical trials.


    Organizational Affiliation

    Roche Palo Alto LLC, 3431 Hillview Avenue, R6-123, Palo Alto, California 94304, USA. David-M.Goldstein@roche.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-Activated Protein Kinase 14A372Homo sapiensMutation(s): 0 
Gene Names: MAPK14CSBPCSBP1CSBP2MXI2CSPB1SAPK2A
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.24 (UniProt)
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
PQB
Query on PQB

Download Ideal Coordinates CCD File 
B [auth A][5-AMINO-1-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL](3-{[(2R)-2,3-DIHYDROXYPROPYL]OXY}PHENYL)METHANONE
C19 H18 F N3 O4
IJDQETGUEUJVTB-HNNXBMFYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PQB BindingDB:  2GFS IC50: min: 180, max: 700 (nM) from 5 assay(s)
PDBBind:  2GFS IC50: 700 (nM) from 1 assay(s)
Binding MOAD:  2GFS IC50: 700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.292α = 90
b = 86.48β = 90
c = 124.055γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description