3FPM

Crystal Structure of a Squarate Inhibitor bound to MAPKAP Kinase-2

• PDB DOI: https://doi.org/10.2210/pdb3FPM/pdb

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


• Deposited: 2009-01-05 Released: 2009-04-07 
• Deposition Author(s): Parris, K.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.337 
• R-Value Work: 0.282 
• R-Value Observed: 0.284 

Starting Model: experimental

Literature

Identification and SAR of squarate inhibitors of mitogen activated protein kinase-activated protein kinase 2 (MK-2)

Lovering, F., Kirincich, S., Wang, W., Combs, K., Resnick, L., Sabalski, J.E., Butera, J., Liu, J., Parris, K., Telliez, J.B.

(2009) Bioorg Med Chem 17: 3342-3351

• PubMed: 19364658 
• DOI: https://doi.org/10.1016/j.bmc.2009.03.041
• Primary Citation of Related Structures:  
  3FPM


• PubMed Abstract: 
  

  A novel series of inhibitors for mitogen activated protein kinase-activated protein kinase 2 (MK-2) are reported. These squarate based inhibitors were identified via a high-throughput screen. An MK2 co-structure with the starting ligand was obtained and a structure based approach was followed to optimize potency and selectivity.

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Organizational Affiliation: 

Chemical Sciences, Wyeth Research, Cambridge, MA 02140, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.95 kDa 
• Atom Count: 2,271 
• Modelled Residue Count: 283 
• Deposited Residue Count: 325 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAP kinase-activated protein kinase 2	A	325	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
793	B [auth A]	3-{[(1R)-1-phenylethyl]amino}-4-(pyridin-4-ylamino)cyclobut-3-ene-1,2-dione C17 H15 N3 O2 MCBPNFWHHNJTGN-LLVKDONJSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
793	PDBBind:  3FPM	IC50: 8900 (nM) from 1 assay(s)
	BindingDB:  3FPM	IC50: 8900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.337 
• R-Value Work: 0.282 
• R-Value Observed: 0.284 
• Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 254.658	α = 90
b = 254.658	β = 90
c = 254.658	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Parris, K.D.

Revision History  

• Version 1.0: 2009-04-07
  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