8AAU | pdb_00008aau

LIM Domain Kinase 1 (LIMK1) bound to LIMKi3

PDB DOI: https://doi.org/10.2210/pdb8AAU/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2022-07-03 Released: 2022-08-10
Deposition Author(s): Mathea, S., Salah, E., Hanke, T., Knapp, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.240 (Depositor), 0.268 (DCC)
R-Value Work:
0.211 (Depositor)
R-Value Observed:
0.213 (Depositor)

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

PubMed: 36136092 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.2c01106
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 36.8 kDa
Atom Count: 2,432
Modeled Residue Count: 291
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIM domain kinase 1	A [auth L]	310	Homo sapiens	Mutation(s): 0 Gene Names: LIMK1, LIMK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53667 (Homo sapiens) Explore P53667 Go to UniProtKB: P53667
PHAROS: P53667 GTEx: ENSG00000106683
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53667
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LH0 (Subject of Investigation/LOI) Query on LH0 Download:Ideal Coordinates CCD File SDF format, chain C [auth L] MOL2 format, chain C [auth L] mmCIF format, chain C [auth L]	C [auth L]	~{N}-[5-[2-[2,6-bis(chloranyl)phenyl]-5-[bis(fluoranyl)methyl]pyrazol-3-yl]-1,3-thiazol-2-yl]-2-methyl-propanamide C₁₇ H₁₄ Cl₂ F₂ N₄ O S IVUGBSGLHRJSSP-UHFFFAOYSA-N		Interactions Focus chain C [auth L] Interactions & Density Focus chain C [auth L]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain E [auth L] SDF format, chain D [auth L] MOL2 format, chain F [auth L] MOL2 format, chain E [auth L] MOL2 format, chain D [auth L] mmCIF format, chain F [auth L] mmCIF format, chain E [auth L] mmCIF format, chain D [auth L]	D [auth L], E [auth L], F [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Interactions & Density Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth L] MOL2 format, chain B [auth L] mmCIF format, chain B [auth L]	B [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth L] Interactions & Density Focus chain B [auth L]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth L] MOL2 format, chain G [auth L] mmCIF format, chain G [auth L]	G [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth L] Interactions & Density Focus chain G [auth L]