9KTK image
Deposition Date 2024-12-02
Release Date 2025-06-25
Last Version Date 2025-06-25
Entry Detail
PDB ID:
9KTK
Title:
Crystal structure of human SIRT3 with its activator SKLB-11A
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.49 Å
R-Value Free:
0.34
R-Value Work:
0.26
R-Value Observed:
0.26
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Gene (Uniprot):SIRT3
Chain IDs:A, B, C, D
Chain Length:277
Number of Molecules:4
Biological Source:Homo sapiens
Primary Citation
Unraveling Small Molecule-Mediated Sirtuin 3 Activation at a Distinct Binding Site for Cardioprotective Therapies.
Acs Cent.Sci. 11 704 718 (2025)
PMID: 40454347 DOI: 10.1021/acscentsci.5c00023

Abstact

Sirtuin 3 (SIRT3), a pivotal mitochondrial deacetylase, plays a critical role in restoring mitochondrial function, particularly through the activation of autophagy. Despite its promise as a cardioprotective target, developing SIRT3 activators and their therapeutic applications remains challenging. Here, we report the identification of SKLB-11A, a SIRT3 activator with submicromolar affinity and high efficacy. Structural and mutagenesis analyses revealed a unique allosteric site for SKLB-11A in SIRT3, where a conformational change in Leu298 drives its potent activation. Subsequent studies demonstrated that SKLB-11A drives autophagy/mitophagy signaling pathways, effectively preventing mitochondrial dysfunction, and improving cardiac dysfunction in both doxorubicin (Dox)-induced cardiotoxicity and myocardial ischemia/reperfusion (I/R) models. Collectively, our data highlight the potential of pharmacological SIRT3 activation as an effective therapeutic strategy for cardioprotection. SKLB-11A, as a first-in-class SIRT3 allosteric activator with a distinct binding mode, not only offers a valuable tool for exploring the physiological and pathological roles of SIRT3 deacetylation but also holds promise for the development of targeted cardioprotective therapies.

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