3ZSI

X-ray structure of p38alpha bound to VX-745

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

X-ray structure of p38 alpha bound to TAK-715: comparison with three classic inhibitors.

Azevedo, R., van Zeeland, M., Raaijmakers, H., Kazemier, B., de Vlieg, J., Oubrie, A.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1041-1050

  • DOI: 10.1107/S090744491201997X
  • Primary Citation of Related Structures:  
    3ZSG, 3ZSH, 3ZSI, 3ZS5

  • PubMed Abstract: 

    • The p38α mitogen-activated protein kinase regulates the synthesis of pro-inflammatory cytokines in response to stimulation by a diverse set of stress signals. Various different chemotypes and clinical candidates that inhibit p38α function have been reported over the years ...

    The p38α mitogen-activated protein kinase regulates the synthesis of pro-inflammatory cytokines in response to stimulation by a diverse set of stress signals. Various different chemotypes and clinical candidates that inhibit p38α function have been reported over the years. In this publication, the novel structure of p38α cocrystallized with the clinical candidate TAK-715 is reported. Owing to the impact of crystallization conditions on the conformation of protein kinases (and in particular p38α), the structures of complexes of p38α with SB-203580, SCIO-469 and VX-745 have also been determined to enable in-depth comparison of ligand-induced protein conformations. The impact of experimental conditions on p38α-inhibitor complex structures, most importantly soaking versus cocrystallization, is discussed. Analysis of the structures and quantification of the protein-ligand interactions couples ligand-induced protein conformations to the number of interactions and to inhibitor selectivity against the human kinome. This shows that for the design of novel kinase inhibitors, selectivity is best obtained through maximization of the number of interactions throughout the ATP pocket and the exploitation of specific features in the active site.

    Organizational Affiliation: 

    Merck Research Laboratories, MSD, PO Box 20, 5340 BH Oss, The Netherlands.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MITOGEN-ACTIVATED PROTEIN KINASE 14 A362Homo sapiensMutation(s): 0 
Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS:  Q16539
GTEx:  ENSG00000112062
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
52P
Query on 52P
Download Ideal Coordinates 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
BOG
Query on BOG
Download Ideal Coordinates CCD File 
A
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.55α = 90
b = 73.65β = 90
c = 76.57γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2012-08-15
    Changes: Database references
  • Version 1.3: 2018-02-07
    Changes: Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary