7QHG

LIM domain kinase 2 (LIMK2) in complex with TH-470


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Development and Characterization of Type I, Type II, and Type III LIM-Kinase Chemical Probes.

Hanke, T.Mathea, S.Woortman, J.Salah, E.Berger, B.T.Tumber, A.Kashima, R.Hata, A.Kuster, B.Muller, S.Knapp, S.

(2022) J Med Chem 65: 13264-13287

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01106
  • Primary Citation of Related Structures:  
    7QHG, 8AAU

  • PubMed Abstract: 

    LIMKs are important regulators of actin and microtubule dynamics, and they play essential roles in many cellular processes. Deregulation of LIMKs has been linked to the development of diverse diseases, including cancers and cognitive disabilities, but well-characterized inhibitors known as chemical probes are still lacking. Here, we report the characterization of three highly selective LIMK1/2 inhibitors covering all canonical binding modes (type I/II/III) and the structure-based design of the type II/III inhibitors. Characterization of these chemical probes revealed a low nanomolar affinity for LIMK1/2, and all inhibitors 1 ( LIMKi3 ; type I), 48 ( TH470 ; type II), and 15 ( TH257 ; type III) showed excellent selectivity in a comprehensive scanMAX kinase selectivity panel. Phosphoproteomics revealed remarkable differences between type I and type II inhibitors compared with the allosteric inhibitor 15 . In phenotypic assays such as neurite outgrowth models of fragile X-chromosome, 15 showed promising activity, suggesting the potential application of allosteric LIMK inhibitors treating this orphan disease.


  • Organizational Affiliation

    Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LIM domain kinase 2
A, B
305Homo sapiensMutation(s): 0 
Gene Names: LIMK2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53671 (Homo sapiens)
Explore P53671 
Go to UniProtKB:  P53671
PHAROS:  P53671
GTEx:  ENSG00000182541 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53671
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T3B (Subject of Investigation/LOI)
Query on T3B

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
2-(2-methylpropanoylamino)-~{N}-[2-[(phenylmethyl)-[4-(phenylsulfamoyl)phenyl]carbonyl-amino]ethyl]-1,3-thiazole-5-carboxamide
C30 H31 N5 O5 S2
YVPYJSSYGACUSE-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
T3B BindingDB:  7QHG Kd: 231 (nM) from 1 assay(s)
IC50: min: 5.5, max: 646 (nM) from 7 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63α = 90
b = 66.692β = 97.961
c = 82.925γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description