8ELC

Human JNK2 bound to covalent inhibitor YL2056


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Development of a Covalent Inhibitor of c-Jun N-Terminal Protein Kinase (JNK) 2/3 with Selectivity over JNK1.

Lu, W.Liu, Y.Gao, Y.Geng, Q.Gurbani, D.Li, L.Ficarro, S.B.Meyer, C.J.Sinha, D.You, I.Tse, J.He, Z.Ji, W.Che, J.Kim, A.Y.Yu, T.Wen, K.Anderson, K.C.Marto, J.A.Westover, K.D.Zhang, T.Gray, N.S.

(2023) J Med Chem 66: 3356-3371

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01834
  • Primary Citation of Related Structures:  
    7N8T, 8ELC

  • PubMed Abstract: 

    The c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinase (MAPK) family, which includes JNK1-JNK3. Interestingly, JNK1 and JNK2 show opposing functions, with JNK2 activity favoring cell survival and JNK1 stimulating apoptosis. Isoform-selective small molecule inhibitors of JNK1 or JNK2 would be useful as pharmacological probes but have been difficult to develop due to the similarity of their ATP binding pockets. Here, we describe the discovery of a covalent inhibitor YL5084, the first such inhibitor that displays selectivity for JNK2 over JNK1. We demonstrated that YL5084 forms a covalent bond with Cys116 of JNK2, exhibits a 20-fold higher K inact / K I compared to that of JNK1, and engages JNK2 in cells. However, YL5084 exhibited JNK2-independent antiproliferative effects in multiple myeloma cells, suggesting the existence of additional targets relevant in this context. Thus, although not fully optimized, YL5084 represents a useful chemical starting point for the future development of JNK2-selective chemical probes.


  • Organizational Affiliation

    Department of Chemical and Systems Biology, Chem-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 9424Homo sapiensMutation(s): 0 
Gene Names: MAPK9JNK2PRKM9SAPK1A
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45984 (Homo sapiens)
Explore P45984 
Go to UniProtKB:  P45984
PHAROS:  P45984
GTEx:  ENSG00000050748 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45984
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y56 (Subject of Investigation/LOI)
Query on Y56

Download Ideal Coordinates CCD File 
B [auth A]4-(dimethylamino)-N-{4-[(3S)-3-({4-[(8R)-2-phenylpyrazolo[1,5-a]pyridin-3-yl]pyrimidin-2-yl}amino)pyrrolidine-1-carbonyl]phenyl}butanamide
C34 H36 N8 O2
HDSKLOGUAXMLMX-MHZLTWQESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.235α = 90
b = 65.761β = 90
c = 94.117γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Welch FoundationUnited StatesI-1829
American Cancer SocietyUnited StatesRSG-18-039-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary