RCSB PDB - 8VTF: A structural study of selectivity mechanisms for JNK3 and p38 alpha with indazole scaffold probing compounds

 8VTF

A structural study of selectivity mechanisms for JNK3 and p38 alpha with indazole scaffold probing compounds

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-01-26 Released: 2025-01-29 
  • Deposition Author(s): Park, H., Feng, Y.
  • Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

A structural study of selectivity mechanisms for JNK3 and p38 alpha with indazole scaffold probing compounds

Park, H.Feng, Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10464Homo sapiensMutation(s): 0 
Gene Names: MAPK10JNK3JNK3APRKM10SAPK1B
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
PHAROS:  P53779
GTEx:  ENSG00000109339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53779
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ACP (Subject of Investigation/LOI)
Query on A1ACP

Download Ideal Coordinates CCD File 
B [auth A](4P)-4-[6-fluoro-5-(2-methoxyanilino)-1H-indazol-1-yl]-N-(oxetan-3-yl)thiophene-2-carboxamide
C22 H19 F N4 O3 S
GYCODKDGFRRIIQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.762α = 90
b = 71.242β = 90
c = 107.769γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1ACPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release