9KTK | pdb_00009ktk

Crystal structure of human SIRT3 with its activator SKLB-11A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.340 (Depositor), 0.339 (DCC) 
  • R-Value Work: 
    0.262 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 
    0.266 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Unraveling Small Molecule-Mediated Sirtuin 3 Activation at a Distinct Binding Site for Cardioprotective Therapies.

Zhang, D.Zhang, J.Wu, C.Xiao, Y.Ji, L.Hu, J.Ding, J.Li, T.Zhang, Y.Ouyang, L.

(2025) ACS Cent Sci 11: 704-718

  • DOI: https://doi.org/10.1021/acscentsci.5c00023
  • Primary Citation Related Structures: 
    9KTK

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, Laboratory of Neuro-system and Multimorbidity, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.

Macromolecule Content 

  • Total Structure Weight: 124.93 kDa 
  • Atom Count: 8,634 
  • Modeled Residue Count: 1,087 
  • Deposited Residue Count: 1,108 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-3, mitochondrial
A, B, C, D
277Homo sapiensMutation(s): 0 
Gene Names: SIRT3SIR2L3
EC: 2.3.1.286 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens)
Explore Q9NTG7 
Go to UniProtKB:  Q9NTG7
PHAROS:  Q9NTG7
GTEx:  ENSG00000142082 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NTG7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EHU
(Subject of Investigation/LOI)

Query on A1EHU



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
L [auth C],
O [auth D]
methyl 2-azanyl-1-[(4-fluorophenyl)methyl]pyrrolo[3,2-b]quinoxaline-3-carboxylate
C19 H15 F N4 O2
ZIRBXDWXWABLAI-UHFFFAOYSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
J [auth C],
M [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
H [auth B],
K [auth C],
N [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.340 (Depositor), 0.339 (DCC) 
  • R-Value Work:  0.262 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 0.266 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.582α = 90
b = 120.362β = 90
c = 134.974γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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: 2025-06-25
    Type: Initial release