7OVL

Protein kinase MKK7 in complex with methoxycyclohexyl-substituted indazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

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

Optimization of Covalent MKK7 Inhibitors via Crude Nanomole-Scale Libraries.

Gehrtz, P.Marom, S.Buhrmann, M.Hardick, J.Kleinbolting, S.Shraga, A.Dubiella, C.Gabizon, R.Wiese, J.N.Muller, M.P.Cohen, G.Babaev, I.Shurrush, K.Avram, L.Resnick, E.Barr, H.Rauh, D.London, N.

(2022) J Med Chem 65: 10341-10356

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c02206
  • Primary Citation of Related Structures:  
    7OVI, 7OVJ, 7OVK, 7OVL, 7OVM, 7OVN

  • PubMed Abstract: 

    High-throughput nanomole-scale synthesis allows for late-stage functionalization (LSF) of compounds in an efficient and economical manner. Here, we demonstrated that copper-catalyzed azide-alkyne cycloaddition could be used for the LSF of covalent kinase inhibitors at the nanoscale, enabling the synthesis of hundreds of compounds that did not require purification for biological assay screening, thus reducing experimental time drastically. We generated crude libraries of inhibitors for the kinase MKK7, derived from two different parental precursors, and analyzed them via the high-throughput In-Cell Western assay. Select inhibitors were resynthesized, validated via conventional biological and biochemical methods such as western blots and liquid chromatography-mass spectrometry (LC-MS) labeling, and successfully co-crystallized. Two of these compounds showed over 20-fold increased inhibitory activity compared to the parental compound. This study demonstrates that high-throughput LSF of covalent inhibitors at the nanomole-scale level can be an auspicious approach in improving the properties of lead chemical matter.


  • Organizational Affiliation

    Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1XZ (Subject of Investigation/LOI)
Query on 1XZ

Download Ideal Coordinates CCD File 
B [auth A]3-(2~{H}-indazol-3-yl)-~{N}-[[1-[(1~{R},2~{R})-2-methoxycyclohexyl]-1,2,3-triazol-4-yl]methyl]-5-(propanoylamino)benzamide
C27 H31 N7 O3
SQKSGNQRUQLTDE-DNQXCXABSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.23α = 90
b = 67.68β = 90
c = 84.73γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary