8PTA | pdb_00008pta

JNK1 covalently bound to BD837 cyclohexenone based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 
    0.226 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Reversible covalent c-Jun N-terminal kinase inhibitors targeting a specific cysteine by precision-guided Michael-acceptor warheads.

Balint, D.Poti, A.L.Alexa, A.Sok, P.Albert, K.Torda, L.Foldesi-Nagy, D.Csokas, D.Turczel, G.Imre, T.Szarka, E.Fekete, F.Bento, I.Bojtar, M.Palko, R.Szabo, P.Monostory, K.Papai, I.Soos, T.Remenyi, A.

(2024) Nat Commun 15: 8606-8606

  • DOI: https://doi.org/10.1038/s41467-024-52573-2
  • Primary Citation Related Structures: 
    8PT8, 8PT9, 8PTA

  • PubMed Abstract: 

    There has been a surge of interest in covalent inhibitors for protein kinases in recent years. Despite success in oncology, the off-target reactivity of these molecules is still hampering the use of covalent warhead-based strategies. Herein, we disclose the development of precision-guided warheads to mitigate the off-target challenge. These reversible warheads have a complex and cyclic structure with optional chirality center and tailored steric and electronic properties. To validate our proof-of-concept, we modified acrylamide-based covalent inhibitors of c-Jun N-terminal kinases (JNKs). We show that the cyclic warheads have high resilience against off-target thiols. Additionally, the binding affinity, residence time, and even JNK isoform specificity can be fine-tuned by adjusting the substitution pattern or using divergent and orthogonal synthetic elaboration of the warhead. Taken together, the cyclic warheads presented in this study will be a useful tool for medicinal chemists for the deliberate design of safer and functionally fine-tuned covalent inhibitors.


  • Organizational Affiliation
    • Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117, Budapest, Hungary.

Macromolecule Content 

  • Total Structure Weight: 127.97 kDa 
  • Atom Count: 8,442 
  • Modeled Residue Count: 1,057 
  • Deposited Residue Count: 1,098 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 8
A, B, C
366Homo sapiensMutation(s): 1 
Gene Names: MAPK8JNK1PRKM8SAPK1SAPK1C
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45983 (Homo sapiens)
Explore P45983 
Go to UniProtKB:  P45983
PHAROS:  P45983
GTEx:  ENSG00000107643 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45983
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free:  0.226 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.256α = 90
b = 106.256β = 90
c = 99.719γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Development and Innovation Office (NKFIH)HungaryKKP 126963

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references, Structure summary