Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.22 kDa 
• Atom Count: 2854 
• Modelled Residue Count: 326 
• Deposited Residue Count: 362 
• Unique protein chains: 1

3ZSI

X-ray structure of p38alpha bound to VX-745

• PDB DOI: 10.2210/pdb3ZSI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-06-28 Released: 2012-06-13 
• Deposition Author(s): Azevedo, R., van Zeeland, M., Raaijmakers, H., Kazemier, B., Oubrie, A.

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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 

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

• PubMed: 22868770 
• DOI: 10.1107/S090744491201997X
• Primary Citation of Related Structures:  
  3ZS5, 3ZSG, 3ZSH, 3ZSI


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOGEN-ACTIVATED PROTEIN KINASE 14	A	362	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
52P	B [auth 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
BOG	C [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
52P	BindingDB:  3ZSI	Kd: min: 2.8, max: 1.00e+4 (nM) from 3 assay(s)
		IC50: min: 0.8, max: 5300 (nM) from 13 assay(s)

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 = 65.55	α = 90
b = 73.65	β = 90
c = 76.57	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-28 
• Released Date: 2012-06-13 
Deposition Author(s): Azevedo, R., van Zeeland, M., Raaijmakers, H., Kazemier, B., Oubrie, A.

Revision History  

• 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