3K3I

p38alpha bound to novel DGF-out compound PF-00215955


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The design, synthesis and potential utility of fluorescence probes that target DFG-out conformation of p38alpha for high throughput screening binding assay.

Tecle, H.Feru, F.Liu, H.Kuhn, C.Rennie, G.Morris, M.Shao, J.Cheng, A.C.Gikunju, D.Miret, J.Coli, R.Xi, S.H.Clugston, S.L.Low, S.Kazmirski, S.Ding, Y.H.Cao, Q.Johnson, T.L.Deshmukh, G.D.DiNitto, J.P.Wu, J.C.English, J.M.

(2009) Chem Biol Drug Des 74: 547-559

  • DOI: https://doi.org/10.1111/j.1747-0285.2009.00884.x
  • Primary Citation of Related Structures:  
    3K3I, 3K3J

  • PubMed Abstract: 

    The design, synthesis and utility of fluorescence probes that bind to the DFG-out conformation of p38alpha kinase are described. Probes that demonstrate good affinity for p38alpha, have been identified and one of the probes, PF-04438255, has been successfully used in an high throughput screening (HTS) assay to identify two novel non-classical p38alpha inhibitors. In addition, a cascade activity assay was utilized to validate the selective binding of these non-classical kinase inhibitors to the unactive form of the enzyme.


  • Organizational Affiliation

    Pfizer Research Technology Center, 620 Memorial Drive, Cambridge, MA 02139, USA. haile.tecle@pfizer.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14350Homo sapiensMutation(s): 0 
Gene Names: CSBPCSBP1CSBP2CSPB1MAPK14MXI2P38
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JZJ
Query on JZJ

Download Ideal Coordinates CCD File 
B [auth A](3S)-3-[4-(4-bromophenyl)-1H-imidazol-2-yl]-1,2,3,4-tetrahydroisoquinoline
C18 H16 Br N3
ZBOUSWQJXIKQSX-INIZCTEOSA-N
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
Binding Affinity Annotations 
IDSourceBinding Affinity
JZJ PDBBind:  3K3I IC50: 1900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.031α = 90
b = 74.878β = 90
c = 77.617γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description