3HP2

Crystal Structure of Human p38alpha complexed with a pyridinone compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    3HP2, 3HP5

  • 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 bound co-crystals of p38alpha ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A360Homo sapiensMutation(s): 0 
Gene Names: CSBPCSBP1CSBP2CSPB1MAPK14MXI2THP-1SAPK2A
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
GTEx:  ENSG00000112062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P36
Query on P36

Download Ideal Coordinates CCD File 
B [auth A]1-benzyl-4-(benzyloxy)-3-bromopyridin-2(1H)-one
C19 H16 Br N O2
VBZTXJCTVYBOKW-UHFFFAOYSA-N
 Ligand Interaction
I46
Query on I46

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
2-fluoro-4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine
C14 H9 F2 N3
YJCHZVXSPFPKMX-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
P36 PDBBind:  3HP2 IC50: 680 (nM) from 1 assay(s)
BindingDB:  3HP2 IC50: 680 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.246α = 90
b = 74.44β = 90
c = 77.238γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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