3MPT

Crystal structure of P38 kinase in complex with a pyrrole-2-carboxamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3MPT/pdb

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


• Deposited: 2010-04-27 Released: 2010-07-07 
• Deposition Author(s): Somers, D.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.298 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 

Starting Model: experimental

Literature

The discovery and initial optimisation of pyrrole-2-carboxamides as inhibitors of p38alpha MAP kinase.

Down, K., Bamborough, P., Alder, C., Campbell, A., Christopher, J.A., Gerelle, M., Ludbrook, S., Mallett, D., Mellor, G., Miller, D.D., Pearson, R., Ray, K., Solanke, Y., Somers, D.

(2010) Bioorg Med Chem Lett 20: 3936-3940

• PubMed: 20570148 
• DOI: https://doi.org/10.1016/j.bmcl.2010.05.011
• Primary Citation of Related Structures:  
  3MPT


• PubMed Abstract: 
  

  A novel pyrrole-2-carboxamide series of p38alpha inhibitors, discovered through the application of virtual screening, is presented. Following evaluation of activity, selectivity and developability properties of commercially available analogues, a synthesis program enabled rapid assessment of the series' suitability for further lead optimisation studies.

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Organizational Affiliation: 

GlaxoSmithKline R&D, Medicines Research Centre, Stevenage, Hertfordshire, UK. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 43.24 kDa 
• Atom Count: 3,167 
• Modelled Residue Count: 347 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	371	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2 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
1GK	B [auth A]	N-(furan-2-ylmethyl)-4-[(2-methylphenyl)carbonyl]-1H-pyrrole-2-carboxamide C18 H16 N2 O3 UTEGJWUIPAWNBB-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1GK	PDBBind:  3MPT	IC50: 251 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.298 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.376	α = 90
b = 85.859	β = 90
c = 124.463	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
d*TREK	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-07 
Deposition Author(s): Somers, D.O.

Revision History  

• Version 1.0: 2010-07-07
  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