3A2C

Crystal structure of a pyrazolopyrimidine inhibitor complex bound to MAPKAP Kinase-2 (MK2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.288 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural analysis of an MK2-inhibitor complex: insight into the regulation of the secondary structure of the Gly-rich loop by TEI-I01800

Fujino, A.Fukushima, K.Namiki, N.Kosugi, T.Takimoto-Kamimura, M.

(2010) Acta Crystallogr D Biol Crystallogr 66: 80-87

  • DOI: 10.1107/S0907444909046411
  • Primary Citation of Related Structures:  
    3A2C

  • PubMed Abstract: 
  • Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2 or MK2) is a Ser/Thr kinase from the p38 mitogen-activated protein kinase signalling pathway and plays an important role in inflammatory diseases. The crystal structure of the com ...

    Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2 or MK2) is a Ser/Thr kinase from the p38 mitogen-activated protein kinase signalling pathway and plays an important role in inflammatory diseases. The crystal structure of the complex of human MK2 (residues 41-364) with the potent MK2 inhibitor TEI-I01800 (pK(i) = 6.9) was determined at 2.9 A resolution. The MK2 structure in the MK2-TEI-I01800 complex is composed of two domains, as observed for other Ser/Thr kinases; however, the Gly-rich loop in the N-terminal domain forms an alpha-helix structure and not a beta-sheet. TEI-I01800 binds to the ATP-binding site as well as near the substrate-binding site of MK2. Both TEI-I01800 molecules have a nonplanar conformation that differs from those of other MK2 inhibitors deposited in the Protein Data Bank. The MK2-TEI-I01800 complex structure is the first active MK2 with an alpha-helical Gly-rich loop and TEI-I01800 regulates the secondary structure of the Gly-rich loop.


    Organizational Affiliation

    Teijin Institute for Biomedical Research, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 2A, B, C, D, E, F, G, H, I, J, K, L324Homo sapiensMutation(s): 0 
Gene Names: MAPKAPK2
EC: 2.7.11.1
Find proteins for P49137 (Homo sapiens)
Explore P49137 
Go to UniProtKB:  P49137
NIH Common Fund Data Resources
PHAROS  P49137
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PDY
Query on PDY

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
N~7~-(4-ethoxyphenyl)-6-methyl-N~5~-[(3S)-piperidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine
C20 H26 N6 O
WJOUGMPFYANZMI-INIZCTEOSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PDYIC50:  130   nM  BindingDB
PDYKi :  126   nM  PDBBind
PDYIC50:  5000   nM  BindingDB
PDYIC50:  11000   nM  BindingDB
PDYIC50:  7200   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.288 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.157α = 90
b = 180.956β = 90
c = 216.096γ = 90
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance