3HP5

Crystal Structure of Human p38alpha complexed with a pyrimidopyridazinone compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of N-substituted pyridinones as potent and selective inhibitors of p38 kinase.

Selness, S.R.Devraj, R.V.Monahan, J.B.Boehm, T.L.Walker, J.K.Devadas, B.Durley, R.C.Kurumbail, R.Shieh, H.Xing, L.Hepperle, M.Rucker, P.V.Jerome, K.D.Benson, A.G.Marrufo, L.D.Madsen, H.M.Hitchcock, J.Owen, T.J.Christie, L.Promo, M.A.Hickory, B.S.Alvira, E.Naing, W.Blevis-Bal, R.

(2009) Bioorg.Med.Chem.Lett. 19: 5851-5856

  • DOI: 10.1016/j.bmcl.2009.08.082
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The identification and evolution of a series of potent and selective p38 inhibitors is described. p38 inhibitors based on a N-benzyl pyridinone high-throughput screening hit were prepared and their SAR explored. Their design was guided by ligand boun ...

    The identification and evolution of a series of potent and selective p38 inhibitors is described. p38 inhibitors based on a N-benzyl pyridinone high-throughput screening hit were prepared and their SAR explored. Their design was guided by ligand bound co-crystals of p38alpha. These efforts resulted in the identification of 12r and 19 as orally active inhibitors of p38 with significant efficacy in both acute and chronic models of inflammation.


    Organizational Affiliation

    Department of Medicinal Chemistry, Pfizer Corporation, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA. shaun.r.selness@pfizer.com




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
52P
Query on 52P

Download SDF File 
Download CCD File 
A
5-(2,6-dichlorophenyl)-2-[(2,4-difluorophenyl)sulfanyl]-6H-pyrimido[1,6-b]pyridazin-6-one
C19 H9 Cl2 F2 N3 O S
VEPKQEUBKLEPRA-UHFFFAOYSA-N
 Ligand Interaction
I46
Query on I46

Download SDF File 
Download CCD File 
A
2-fluoro-4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine
C14 H9 F2 N3
YJCHZVXSPFPKMX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
52PIC50: 0.8 - 5300 nM (99) BINDINGDB
52PKd: 2.8 - 3.2 nM (100) BINDINGDB
52PIC50: 70 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.045α = 90.00
b = 74.022β = 90.00
c = 76.697γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description