3W55

The structure of ERK2 in complex with FR148083


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Role of a cysteine residue in the active site of ERK and the MAPKK family

Ohori, M.Kinoshita, T.Yoshimura, S.Warizaya, M.Nakajima, H.Miyake, H.

(2007) Biochem.Biophys.Res.Commun. 353: 633-637

  • DOI: 10.1016/j.bbrc.2006.12.083
  • Primary Citation of Related Structures:  2E14

  • PubMed Abstract: 
  • Kinases of mitogen-activated protein kinase (MAPK) cascades, including extracellular signal-regulated protein kinase (ERK), represent likely targets for pharmacological intervention in proliferative diseases. Here, we report that FR148083 inhibits ER ...

    Kinases of mitogen-activated protein kinase (MAPK) cascades, including extracellular signal-regulated protein kinase (ERK), represent likely targets for pharmacological intervention in proliferative diseases. Here, we report that FR148083 inhibits ERK2 enzyme activity and TGFbeta-induced AP-1-dependent luciferase expression with respective IC50 values of 0.08 and 0.05 microM. FR265083 (1'-2' dihydro form) and FR263574 (1'-2' and 7'-8' tetrahydro form) exhibited 5.5-fold less and no activity, respectively, indicating that both the alpha,beta-unsaturated ketone and the conformation of the lactone ring contribute to this inhibitory activity. The X-ray crystal structure of the ERK2/FR148083 complex revealed that the compound binds to the ATP binding site of ERK2, involving a covalent bond to Sgamma of ERK2 Cys166, hydrogen bonds with the backbone NH of Met108, Nzeta of Lys114, backbone C=O of Ser153, Ndelta2 of Asn154, and hydrophobic interactions with the side chains of Ile31, Val39, Ala52, and Leu156. The covalent bond motif in the ERK2/FR148083 complex assures that the inhibitor has high activity for ERK2 and no activity for other MAPKs such as JNK1 and p38MAPKalpha/beta/gamma/delta which have leucine residues at the site corresponding to Cys166 in ERK2. On the other hand, MEK1 and MKK7, kinases of the MAPKK family which also can be inhibited by FR148083, contain a cysteine residue corresponding to Cys166 of ERK2. The covalent binding to the common cysteine residue in the ATP-binding site is therefore likely to play a crucial role in the inhibitory activity for these MAP kinases. These findings on the molecular recognition mechanisms of FR148083 for kinases with Cys166 should provide a novel strategy for the pharmacological intervention of MAPK cascades.


    Organizational Affiliation

    Astellas Pharma Inc., Tokodai 5-2-3, Tsukuba, Ibaraki 300-2698, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 1
A
368Homo sapiensGene 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1FM
Query on 1FM

Download SDF File 
Download CCD File 
A
(3S,5Z,8S,9S,11E)-8,9,16-trihydroxy-14-methoxy-3-methyl-3,4,9,10-tetrahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione
(5Z)-7-Oxozeaenol
C19 H22 O7
NEQZWEXWOFPKOT-BYRRXHGESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FRRIC50: 80 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.870α = 90.00
b = 71.240β = 90.00
c = 120.880γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
CNXrefinement
AMoREphasing
CrystalCleardata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-01-21 
  • Released Date: 2013-02-06 
  • Deposition Author(s): Ohori, M., Kinoshita, T.
  • This entry supersedes: 2E14

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release