5AX3

Crystal structure of ERK2 complexed with allosteric and ATP-competitive inhibitors.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.984 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Identification of allosteric ERK2 inhibitors through in silico biased screening and competitive binding assay

Kinoshita, T.Sugiyama, H.Mori, Y.Takahashi, N.Tomonaga, A.

(2016) Bioorg.Med.Chem.Lett. 26: 955-958

  • DOI: 10.1016/j.bmcl.2015.12.056

  • PubMed Abstract: 
  • Extracellular signal-regulated kinase 2 (ERK2) is a drug target for type 2 diabetes mellitus. A peptide-type ERK2 inhibitor (PEP) was discovered in the previous study through the knowledge-based method and showed physiological effects on the db/db mi ...

    Extracellular signal-regulated kinase 2 (ERK2) is a drug target for type 2 diabetes mellitus. A peptide-type ERK2 inhibitor (PEP) was discovered in the previous study through the knowledge-based method and showed physiological effects on the db/db mice model of type 2 diabetes. Here, the crystal structure showed that PEP bound to the allosteric site without the interruption of the ATP competitive inhibitor binding to ERK2. An in silico biased-screening using the focused library rendered three compounds with inhibitory activity of IC50 <100 μM. Among them, two compounds revealed the concentration-dependent competition with PEP and could be lead compounds for antidiabetic medicine.


    Organizational Affiliation

    Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan. Electronic address: kinotk@b.s.osakafu-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 1
A
368Homo sapiensMutation(s): 0 
Gene Names: MAPK1 (ERK2, PRKM1, PRKM2)
EC: 2.7.11.24
Find proteins for P28482 (Homo sapiens)
Go to Gene View: MAPK1
Go to UniProtKB:  P28482
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
allosteric and ATP-competitive inhibitor
B
12Homo sapiensMutation(s): 0 
Gene Names: STAT3 (APRF)
Find proteins for P40763 (Homo sapiens)
Go to Gene View: STAT3
Go to UniProtKB:  P40763
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5ID
Query on 5ID

Download SDF File 
Download CCD File 
A
(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL
5-IODOTUBERCIDIN
C11 H13 I N4 O4
WHSIXKUPQCKWBY-IOSLPCCCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5IDKi: 530 nM (100) BINDINGDB
5IDIC50: 1200 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.984 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.835α = 90.00
b = 66.465β = 90.00
c = 116.871γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release