7OVK | pdb_00007ovk

Protein kinase MKK7 in complex with 5-bromo-2-hydroxyphenyl-substituted pyrazolopyrimidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.244 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7OVK

Ligand Structure Quality Assessment 


This is version 2.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 36.75 kDa 
  • Atom Count: 2,091 
  • Modeled Residue Count: 256 
  • Deposited Residue Count: 318 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2I5
(Subject of Investigation/LOI)

Query on 2I5



Download:Ideal Coordinates CCD File
C [auth A]1-[(3~{R})-3-[4-azanyl-3-[1-(5-bromanyl-2-oxidanyl-phenyl)-1,2,3-triazol-4-yl]pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one
C21 H22 Br N9 O2
ZXTJFMIWRHTIKC-CYBMUJFWSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.244 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.08α = 90
b = 68.09β = 90
c = 85.08γ = 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: 2022-08-10
    Changes: Database references
  • Version 1.2: 2022-08-17
    Changes: Database references
  • Version 1.3: 2022-09-14
    Changes: Structure summary
  • Version 1.4: 2022-10-12
    Changes: Structure summary
  • Version 2.0: 2023-05-24
    Changes: Non-polymer description
  • Version 2.1: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary