7Z4V | pdb_00007z4v

Structure of Serine-Threonine kinase STK25 in complex with compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 
    0.283 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Z4V

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Targeting non-alcoholic fatty liver disease: Design, X-ray co-crystal structure and synthesis of 'first-in-kind' inhibitors of serine/threonine kinase25.

Kiyeleko, S.Hocine, S.Mautino, G.Kuenemann, M.Nawrotek, A.Miallau, L.Vuillard, L.M.Mirguet, O.Kotschy, A.Hanessian, S.

(2022) Bioorg Med Chem Lett 75: 128950-128950

  • DOI: https://doi.org/10.1016/j.bmcl.2022.128950
  • Primary Citation Related Structures: 
    7Z4V

  • PubMed Abstract: 

    We describe the synthesis of a series of 3-t-butyl 5-aminopyrazole p-substituted arylamides as inhibitors of serine-threonine25 (STK25), an enzyme implicated in the progression of non-alcoholic fatty liver disease (NAFLD). Appending a p-N-pyrrolidinosulphonamide group to the arylamide group led to a 'first-in kind' inhibitor with IC 50  = 228 nM. A co-crystal structure with STK 25 revealed productive interactions which were also reproduced using molecular docking. A new series of triazolo dihydro oxazine carboxamides of 3-t-butyl 5-aminopyrazole was not active against STK25.


  • Organizational Affiliation
    • Department of Chemistry, Université de Montréal, Station Centre-Ville, C.P. 6128, Montreal, QC H3C 3J7, Canada.

Macromolecule Content 

  • Total Structure Weight: 34.36 kDa 
  • Atom Count: 2,549 
  • Modeled Residue Count: 289 
  • Deposited Residue Count: 297 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 25297Homo sapiensMutation(s): 0 
Gene Names: STK25SOK1YSK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O00506 (Homo sapiens)
Explore O00506 
Go to UniProtKB:  O00506
PHAROS:  O00506
GTEx:  ENSG00000115694 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00506
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IB5
(Subject of Investigation/LOI)

Query on IB5



Download:Ideal Coordinates CCD File
B [auth A]~{N}-(5-~{tert}-butyl-1~{H}-pyrazol-3-yl)-4-pyrrolidin-1-ylsulfonyl-benzamide
C18 H24 N4 O3 S
RWSQKAWHFBAQTA-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
IB5 BindingDB:  7Z4V IC50: min: 211, max: 228 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free:  0.283 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.2α = 90
b = 46.413β = 90.56
c = 57.954γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-09-07
    Changes: Database references
  • Version 1.2: 2022-09-14
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary