7B8W | pdb_00007b8w

Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470

PDB DOI: https://doi.org/10.2210/pdb7B8W/pdb

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

Deposited: 2020-12-13 Released: 2022-03-02
Deposition Author(s): Lee, H., Yosaatmadja, Y., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Elkins, J.M.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.286 (Depositor), 0.283 (DCC)
R-Value Work:
0.206 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470

Lee, H., Yosaatmadja, Y., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Elkins, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 146.59 kDa
Atom Count: 8,652
Modeled Residue Count: 1,103
Deposited Residue Count: 1,240
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, B, C, D	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T3B (Subject of Investigation/LOI) Query on T3B Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], J [auth C], K [auth D]	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		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]