5V62

Phospho-ERK2 bound to bivalent inhibitor SBP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Guided Strategy for the Development of Potent Bivalent ERK Inhibitors.

Lechtenberg, B.C.Mace, P.D.Sessions, E.H.Williamson, R.Stalder, R.Wallez, Y.Roth, G.P.Riedl, S.J.Pasquale, E.B.

(2017) ACS Med Chem Lett 8: 726-731

  • DOI: 10.1021/acsmedchemlett.7b00127
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ERK is the effector kinase of the RAS-RAF-MEK-ERK signaling cascade, which promotes cell transformation and malignancy in many cancers and is thus a major drug target in oncology. Kinase inhibitors targeting RAF or MEK are already used for the treatm ...

    ERK is the effector kinase of the RAS-RAF-MEK-ERK signaling cascade, which promotes cell transformation and malignancy in many cancers and is thus a major drug target in oncology. Kinase inhibitors targeting RAF or MEK are already used for the treatment of certain cancers, such as melanoma. Although the initial response to these drugs can be dramatic, development of drug resistance is a major challenge, even with combination therapies targeting both RAF and MEK. Importantly, most resistance mechanisms still rely on activation of the downstream effector kinase ERK, making it a promising target for drug development efforts. Here, we report the design and structural/functional characterization of a set of bivalent ERK inhibitors that combine a small molecule inhibitor that binds to the ATP-binding pocket with a peptide that selectively binds to an ERK protein interaction surface, the D-site recruitment site (DRS). Our studies show that the lead bivalent inhibitor, SBP3, has markedly improved potency compared to the small molecule inhibitor alone. Unexpectedly, we found that SBP3 also binds to several ERK-related kinases that contain a DRS, highlighting the importance of experimentally verifying the predicted specificity of bivalent inhibitors. However, SBP3 does not target any other kinases belonging to the same CMGC branch of the kinome. Additionally, our modular click chemistry inhibitor design facilitates the generation of different combinations of small molecule inhibitors with ERK-targeting peptides.


    Organizational Affiliation

    Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, Florida 32827, United States.,Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States.,Pathology Department, University of California San Diego, La Jolla, California 92093, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 1
A
351Homo 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
Ribosomal protein S6 kinase alpha-1
I
21Homo sapiensMutation(s): 0 
Gene Names: RPS6KA1 (MAPKAPK1A, RSK1)
EC: 2.7.11.1
Find proteins for Q15418 (Homo sapiens)
Go to Gene View: RPS6KA1
Go to UniProtKB:  Q15418
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AKS
Query on AKS

Download SDF File 
Download CCD File 
A
N-(hex-5-yn-1-yl)hexanamide
C12 H21 N O
CJZDJNGNVAVPMZ-UHFFFAOYSA-N
 Ligand Interaction
FRZ
Query on FRZ

Download SDF File 
Download CCD File 
A
5-(2-PHENYLPYRAZOLO[1,5-A]PYRIDIN-3-YL)-1H-PYRAZOLO[3,4-C]PYRIDAZIN-3-AMINE
FR180204
C18 H13 N7
XVECMUKVOMUNLE-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
AZK
Query on AZK
I
L-PEPTIDE LINKINGC6 H14 N4 OLYS
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.327α = 90.00
b = 77.888β = 90.00
c = 152.938γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01CA160457

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence
  • Version 1.2: 2018-04-18
    Type: Advisory, Data collection, Database references