3WI6

Crystal structure of MAPKAP Kinase-2 (MK2) in complex with non-selective inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of the beta-form of human MK2 in complex with the non-selective kinase inhibitor TEI-L03090

Fujino, A.Fukushima, K.Kubota, T.Matsumoto, Y.Takimoto-Kamimura, M.

(2013) Acta Crystallogr.,Sect.F 69: 1344-1348

  • DOI: 10.1107/S1744309113030534

  • PubMed Abstract: 
  • Mitogen-activated protein kinase-activated protein kinase 2 (MK2 or MAPKAP-K2), a serine/threonine kinase from the p38 mitogen-activated protein kinase signalling pathway, plays an important role in the production of TNF-α and other cytokines. In a p ...

    Mitogen-activated protein kinase-activated protein kinase 2 (MK2 or MAPKAP-K2), a serine/threonine kinase from the p38 mitogen-activated protein kinase signalling pathway, plays an important role in the production of TNF-α and other cytokines. In a previous report, it was shown that MK2 in complex with the selective inhibitor TEI-I01800 adopts an α-helical glycine-rich loop that is induced by the stable nonplanar conformer of TEI-I01800. To understand the mechanism of the structural change, the structure of MK2 bound to TEI-L03090, which lacks the key substituent found in TEI-I01800, was determined. MK2-TEI-L03090 has a β-sheet glycine-rich loop in common with other kinases, as predicted. This result suggests that a small compound can induce a drastic conformational change in the target protein structure and can be used to design potent and selective inhibitors.


    Organizational Affiliation

    Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAP kinase-activated protein kinase 2
A, B, C, D, E, F
324Homo sapiensMutation(s): 0 
Gene Names: MAPKAPK2
EC: 2.7.11.1
Find proteins for P49137 (Homo sapiens)
Go to Gene View: MAPKAPK2
Go to UniProtKB:  P49137
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YRZ
Query on YRZ

Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-[(3S)-piperidin-3-yl]-7,8-dihydro-6H-pyrazolo[1,5-a]pyrrolo[3,2-e]pyrimidin-5-amine
C13 H18 N6
BRLBLOAZCZCBIY-VIFPVBQESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YRZIC50: 4700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.240 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 180.061α = 90.00
b = 179.684β = 90.00
c = 254.101γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-18
    Type: Initial release