3IPH

Crystal structure of p38 in complex with a biphenylamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

p38alpha mitogen-activated protein kinase inhibitors: optimization of a series of biphenylamides to give a molecule suitable for clinical progression.

Aston, N.M.Bamborough, P.Buckton, J.B.Edwards, C.D.Holmes, D.S.Jones, K.L.Patel, V.K.Smee, P.A.Somers, D.O.Vitulli, G.Walker, A.L.

(2009) J.Med.Chem. 52: 6257-6269

  • DOI: 10.1021/jm9004779

  • PubMed Abstract: 
  • p38alpha MAP kinase is a key anti-inflammatory target for rheumatoid arthritis, influencing biosynthesis of pro-inflammatory cytokines TNFalpha and IL-1beta at a translational and transcriptional level. In this paper, we describe how we have optimize ...

    p38alpha MAP kinase is a key anti-inflammatory target for rheumatoid arthritis, influencing biosynthesis of pro-inflammatory cytokines TNFalpha and IL-1beta at a translational and transcriptional level. In this paper, we describe how we have optimized a series of novel p38alpha/beta inhibitors using crystal structures of our inhibitors bound to p38alpha, classical medicinal chemistry, and modeling of virtual libraries to derive a molecule suitable for progression into clinical development.


    Organizational Affiliation

    GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Rd, Stevenage, Hertfordshire SG1 2NY, UK.




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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
G11
Query on G11

Download SDF File 
Download CCD File 
A
6-[5-(cyclopropylcarbamoyl)-2-methylphenyl]-N-(cyclopropylmethyl)pyridine-3-carboxamide
C21 H23 N3 O2
WIXHEGLMUQGJCC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G11Ki: 25.1 nM (100) BINDINGDB
G11IC50: 316.2 nM (100) BINDINGDB
G11Ki: 25.1 nM BINDINGMOAD
G11Ki: 25.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.753α = 90.00
b = 85.688β = 90.00
c = 125.206γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-08-17 
  • Released Date: 2009-11-24 
  • Deposition Author(s): Somers, D.O.

Revision History 

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description