9HZ0 | pdb_00009hz0

Protein kinase MKK7 in complex with K221 targeting compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.263 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Computational Design of Lysine Targeting Covalent Binders Using Rosetta.

Tivon, B.Wiese, J.Muller, M.P.Gabizon, R.Rauh, D.London, N.

(2025) J Chem Inf Model 65: 5612-5622

  • DOI: https://doi.org/10.1021/acs.jcim.5c00212
  • Primary Citation of Related Structures:  
    9HZ0

  • PubMed Abstract: 

    Chemical probes that form a covalent bond with their target protein have been established as a powerful tool for investigating proteins and modulating their activity, but until recently were mostly targeting cysteine residues. Covalent binders that target lysine residues are increasingly reported. Covalent binding to lysine involves challenges such as the increased p K a of the side chain and its considerable flexibility. Here, we describe two computational methods to derivatize lysine-binding covalent small-molecules based on known noncovalent binders, approaching the design problem from two opposite directions. In a "ligand-side" approach, we scan different ligand positions to install an electrophile and dock these derivatized ligands into the target protein. In a "protein-side" approach, we install an electrophile on the target lysine and model its conformational space to find suitable installation vectors on the ligand. We applied both of these protocols retrospectively to a data set of electrophilic ligands and to a data set of vitamin B6 covalently bound to a receptor lysine residue. Our ligand-side protocol successfully identified the known covalent binder in 80% and 86% of cases, while the protein-side protocol achieved identification rates of 56% and 82%, respectively. We prospectively validated these protocols by designing and testing a new lysine-targeting MKK7 inhibitor. Mass-spectrometry and crystallography validated the covalent binding to the target lysine. Applying these protocols to a data set of known kinase inhibitors identified high-confidence covalent candidates for more than 200 human kinases, demonstrating the potential impact of our protocols.


  • Organizational Affiliation
    • Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 7318Homo sapiensMutation(s): 0 
Gene Names: MAP2K7JNKK2MEK7MKK7PRKMK7SKK4
EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for O14733 (Homo sapiens)
Explore O14733 
Go to UniProtKB:  O14733
PHAROS:  O14733
GTEx:  ENSG00000076984 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14733
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IY7 (Subject of Investigation/LOI)
Query on A1IY7

Download Ideal Coordinates CCD File 
B [auth A]5-(2~{H}-indazol-3-yl)-2-methyl-phenol
C14 H12 N2 O
NWZPHRUFHASTQV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.263 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.01α = 90
b = 69.14β = 90
c = 83.53γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Regional Development FundEuropean UnionEFRE-800400
Other governmentNW21-062C
German Federal Ministry for Education and ResearchGermany01ZX2201A

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references
  • Version 1.2: 2025-06-18
    Changes: Database references