2P3G

Crystal structure of a pyrrolopyridine inhibitor bound to MAPKAP Kinase-2

• PDB DOI: https://doi.org/10.2210/pdb2P3G/pdb

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


• Deposited: 2007-03-08 Released: 2007-06-12 
• Deposition Author(s): Kurumbail, R.G., Caspers, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.374 
• R-Value Work: 0.300 
• R-Value Observed: 0.303 

Starting Model: experimental

Literature

Pyrrolopyridine Inhibitors of Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MK-2).

Anderson, D.R., Meyers, M.J., Vernier, W.F., Mahoney, M.W., Kurumbail, R.G., Caspers, N., Poda, G.I., Schindler, J.F., Reitz, D.B., Mourey, R.J.

(2007) J Med Chem 50: 2647-2654

• PubMed: 17480064 
• DOI: https://doi.org/10.1021/jm0611004
• Primary Citation of Related Structures:  
  2P3G


• PubMed Abstract: 
  

  A new class of potent kinase inhibitors selective for mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2 or MK-2) for the treatment of rheumatoid arthritis has been prepared and evaluated. These inhibitors have IC50 values as low as 10 nM against the target and have good selectivity profiles against a number of kinases including CDK2, ERK, JNK, and p38. These MK-2 inhibitors have been shown to suppress TNFalpha production in U397 cells and to be efficacious in an acute inflammation model. The structure-activity relationships of this series, the selectivity for MK-2 and their activity in both in vitro and in vivo models are discussed. The observed selectivity is discussed with the aid of an MK-2/inhibitor crystal structure.

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Organizational Affiliation: 

Pfizer Global Research and Development, St. Louis Laboratories, 700 Chesterfield Parkway W, Chesterfield, Missouri 63017, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.21 kDa 
• Atom Count: 2,321 
• Modelled Residue Count: 282 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAP kinase-activated protein kinase 2	A [auth X]	327	Homo sapiens	Mutation(s): 0  Gene Names: MAPKAPK2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49137 (Homo sapiens) Explore P49137  Go to UniProtKB:  P49137
PHAROS:  P49137 GTEx:  ENSG00000162889

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F10	B [auth X]	2-[2-(2-FLUOROPHENYL)PYRIDIN-4-YL]-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE C18 H14 F N3 O XJJYJNMNYDNXNO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
F10	BindingDB:  2P3G	IC50: min: 126, max: 8900 (nM) from 3 assay(s)
		EC50: min: 372, max: 2700 (nM) from 2 assay(s)
	PDBBind:  2P3G	IC50: 126 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.374 
• R-Value Work: 0.300 
• R-Value Observed: 0.303 
• Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 253.941	α = 90
b = 253.941	β = 90
c = 253.941	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-12 
Deposition Author(s): Kurumbail, R.G., Caspers, N.

Revision History  

• Version 1.0: 2007-06-12
  Type: Initial release
  
• Version 1.1: 2008-03-05
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description