8P7J

Crystal structure of MAP2K6 with a covalent compound GCL96


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.257 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Probing the Protein Kinases' Cysteinome by Covalent Fragments.

Wang, G.Seidler, N.J.Rohm, S.Pan, Y.Liang, X.J.Haarer, L.Berger, B.T.Sivashanmugam, S.A.Wydra, V.R.Forster, M.Laufer, S.A.Chaikuad, A.Gehringer, M.Knapp, S.

(2024) Angew Chem Int Ed Engl : e202419736-e202419736

  • DOI: https://doi.org/10.1002/anie.202419736
  • Primary Citation of Related Structures:  
    8P7J, 8PM3, 9F32, 9F81, 9HHW

  • PubMed Abstract: 

    Protein kinases are important drug targets, yet specific inhibitors have been developed for only a fraction of the more than 500 human kinases. A major challenge in designing inhibitors for highly related kinases is selectivity. Unlike their non-covalent counterparts, covalent inhibitors offer the advantage of selectively targeting structurally similar kinases by modifying specific protein side chains, particularly non-conserved cysteines. Previously, covalent fragment screens yielded potent and selective compounds for individual kinases such as ERK1/2 but have not been applied to the broader kinome. Furthermore, many of the accessible cysteine positions have not been addressed so far. Here, we outline a generalizable approach to sample ATP-site cysteines with fragment-like covalent inhibitors. We present the development of a kinase-focused fragment library and its systematic screening against a curated selection of 47 kinases, with 60 active site-proximal cysteines using LC/MS and differential scanning fluorimetry (DSF) assays, followed by hit validation through various complementary techniques. Our findings expand the repertoire of targetable cysteines within protein kinases, provide insight into unique binding modes identified from crystal structures and deliver isoform-specific hits with promising profiles as starting points for the development of highly potent and selective covalent inhibitors.


  • Organizational Affiliation

    Goethe-Universitat Frankfurt am Main Fachbereich 14 Biochemie Chemie und Pharmazie, Institute for Pharmaceutical Chemistry, GERMANY.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 6
A, B
290Homo sapiensMutation(s): 2 
Gene Names: MAP2K6MEK6MKK6PRKMK6SKK3
EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for P52564 (Homo sapiens)
Explore P52564 
Go to UniProtKB:  P52564
PHAROS:  P52564
GTEx:  ENSG00000108984 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52564
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.257 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.712α = 90
b = 96.92β = 90
c = 104.806γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted X3KClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Structural Genomics Consortium (SGC)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-08-09
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-01-08
    Changes: Database references