6G54

Crystal structure of ERK2 covalently bound to SM1-71


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome.

Rao, S.Gurbani, D.Du, G.Everley, R.A.Browne, C.M.Chaikuad, A.Tan, L.Schroder, M.Gondi, S.Ficarro, S.B.Sim, T.Kim, N.D.Berberich, M.J.Knapp, S.Marto, J.A.Westover, K.D.Sorger, P.K.Gray, N.S.

(2019) Cell Chem Biol 26: 818

  • DOI: 10.1016/j.chembiol.2019.02.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Covalent kinase inhibitors, which typically target cysteine residues, represent an important class of clinically relevant compounds. Approximately 215 kinases are known to have potentially targetable cysteines distributed across 18 spatially distinct ...

    Covalent kinase inhibitors, which typically target cysteine residues, represent an important class of clinically relevant compounds. Approximately 215 kinases are known to have potentially targetable cysteines distributed across 18 spatially distinct locations proximal to the ATP-binding pocket. However, only 40 kinases have been covalently targeted, with certain cysteine sites being the primary focus. To address this disparity, we have developed a strategy that combines the use of a multi-targeted acrylamide-modified inhibitor, SM1-71, with a suite of complementary chemoproteomic and cellular approaches to identify additional targetable cysteines. Using this single multi-targeted compound, we successfully identified 23 kinases that are amenable to covalent inhibition including MKNK2, MAP2K1/2/3/4/6/7, GAK, AAK1, BMP2K, MAP3K7, MAPKAPK5, GSK3A/B, MAPK1/3, SRC, YES1, FGFR1, ZAK (MLTK), MAP3K1, LIMK1, and RSK2. The identification of nine of these kinases previously not targeted by a covalent inhibitor increases the number of targetable kinases and highlights opportunities for covalent kinase inhibitor development.


    Organizational Affiliation

    California Institute for Quantitative Biosciences, University of California, Berkeley, United States.,Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.,p53 Laboratory , ASTAR (Agency for Science, Technology and Research) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648 . Email: cjbrown@p53lab.a-star.edu.sg ; Tel: +65 6478 8273.,Ipsen Innovation , 5, Avenue du Canada , Les Ulis , France 91940 . Email: sergeauvin@gmail.com ; Tel: +33 160 922481.,Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; German Cancer Network (DKTK), Frankfurt Site, 60438 Frankfurt am Main, Germany.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: nathanael_gray@dfci.harvard.edu.,the Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224, radisky.evette@mayo.edu.,School of Biological Sciences , Nanyang Technological University , 50 Nanyang Drive , Singapore 637551.,From the Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA.,Howard Hughes Medical Institute, University of California, Berkeley, United States.,RIKEN Program for Drug Discovery and Medical Technology Platforms , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,Department of Biotechnology , The University of Tokyo , 1-1-1 Yayoi , Bunkyo-ku, Tokyo 113-8657 , Japan.,From the Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, papo@bgu.ac.il.,the Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224.,Bioinformatics Institute , ASTAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 . Email: chandra@bii.a-star.edu.sg ; Tel: +65 6478 8273.,David Geffen School of Medicine, University of California Los Angeles and Greater West Los Angeles Health Care System, Los Angeles, CA 90095, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,the National Institute for Biotechnology in the Negev (NIBN), Beer-Sheva 84105, Israel.,the Molecular Biophysics and Integrated Bioimaging Division, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and.,Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal.,Ipsen Bioscience , 650 East Kendall Street , Cambridge , MA 02142 , USA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,the Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida 32224.,Department of Agrifood Production and Environmental Sciences, University of Florence, Florence, Italy.,Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany.,California NanoSystems Institute, University California Los Angeles, Los Angeles, CA 90095, USA.,Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.,Division of Molecular Biotherapy, Cancer Chemotherapy Center , Japanese Foundation for Cancer Research , 3-8-31 Ariake , Koto-ku, Tokyo 135-8850 , Japan.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Porto, Portugal.,Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543.,Department of Molecular and Cell Biology, University of California, Berkeley, United States.,NDBio Therapeutics Inc., Incheon 21984, Republic of Korea.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: peter_sorger@hms.harvard.edu.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 1
A
361Homo 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
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6H3
Query on 6H3

Download SDF File 
Download CCD File 
A
N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]phenyl}propanamide
C24 H28 Cl N7 O
IIMJCIGRKJCCHT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.751α = 90.00
b = 91.751β = 90.00
c = 99.305γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-05-01
    Type: Data collection, Database references
  • Version 1.2: 2019-07-03
    Type: Data collection, Database references