6NBS

WT ERK2 with compound 2507-8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A Novel Class of Common Docking Domain Inhibitors That Prevent ERK2 Activation and Substrate Phosphorylation.

Sammons, R.M.Perry, N.A.Li, Y.Cho, E.J.Piserchio, A.Zamora-Olivares, D.P.Ghose, R.Kaoud, T.S.Debevec, G.Bartholomeusz, C.Gurevich, V.V.Iverson, T.M.Giulianotti, M.Houghten, R.A.Dalby, K.N.

(2019) ACS Chem Biol 14: 1183-1194

  • DOI: https://doi.org/10.1021/acschembio.9b00093
  • Primary Citation of Related Structures:  
    6NBS

  • PubMed Abstract: 

    Extracellular signal-regulated kinases (ERK1/2) are mitogen-activated protein kinases (MAPKs) that play a pro-tumorigenic role in numerous cancers. ERK1/2 possess two protein-docking sites that are distinct from the active site: the D-recruitment site (DRS) and the F-recruitment site. These docking sites facilitate substrate recognition, intracellular localization, signaling specificity, and protein complex assembly. Targeting these sites on ERK in a therapeutic context may overcome many problems associated with traditional ATP-competitive inhibitors. Here, we identified a new class of inhibitors that target the ERK DRS by screening a synthetic combinatorial library of more than 30 million compounds. The screen detects the competitive displacement of a fluorescent peptide from the DRS of ERK2. The top molecular scaffold from the screen was optimized for structure-activity relationship by positional scanning of different functional groups. This resulted in 10 compounds with similar binding affinities and a shared core structure consisting of a tertiary amine hub with three functionalized cyclic guanidino branches. Compound 2507-1 inhibited ERK2 from phosphorylating a DRS-targeting substrate and prevented the phosphorylation of ERK2 by a constitutively active MEK1 (MAPK/ERK kinase 1) mutant. Interaction between an analogue, 2507-8, and the ERK2 DRS was confirmed by nuclear magnetic resonance and X-ray crystallography. 2507-8 forms critical interactions at the common docking domain residue Asp319 via an arginine-like moiety that is shared by all 10 hits, suggesting a common binding mode. The structural and biochemical insights reported here provide the basis for developing new ERK inhibitors that are not ATP-competitive but instead function by disrupting critical protein-protein interactions.


  • Organizational Affiliation

    Torrey Pines Institute for Molecular Studies , Port St. Lucie , Florida 34987 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1367Rattus norvegicusMutation(s): 0 
Gene Names: Mapk1Erk2MapkPrkm1
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens)
Explore P28482 
Go to UniProtKB:  P28482
PHAROS:  P28482
GTEx:  ENSG00000100030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28482
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KJ4
Query on KJ4

Download Ideal Coordinates CCD File 
E [auth A]N-{3-[(2Z,4S)-1-(2-{[2-(2-amino-1H-imidazol-1-yl)ethyl](methyl)amino}ethyl)-3-(3-cyclohexylpropyl)-2-iminoimidazolidin-4-yl]propyl}guanidine
C24 H46 N10
LDGRSKSJJICZTA-QTEAAIINSA-N
KJ7
Query on KJ7

Download Ideal Coordinates CCD File 
D [auth A](5S)-5-benzyl-4,5-dihydro-1H-imidazol-2-amine
C10 H13 N3
OZKGTJHTWRZQLA-VIFPVBQESA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.895α = 90
b = 71.242β = 109.37
c = 60.167γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States16PRE30180007
American Heart AssociationUnited States18PRE34030017

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2021-09-08
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2023-10-11
    Changes: Data collection, Refinement description