SMTL ID : 9ktk.2 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.142, C.145, C.166, C.169, T.170, G.171 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.142, A:C.145, A:C.166, A:C.169 ZN.3: 4 residues within 4Å: Chain B: C.142, C.145, C.166, C.169 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.142, B:C.145, B:C.166, B:C.169

2 x 01: methyl 2-azanyl-1-[(4-fluorophenyl)methyl]pyrrolo[3,2-b]quinoxaline-3-carboxylate

01.2: 10 residues within 4Å: Chain A: R.44, E.63, F.66, I.116, H.134, I.177, V.178, F.179, F.180 Chain B: Y.61 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.63, A:V.178, A:F.180 Hydrogen bonds: A:V.178 Salt bridges: A:H.134 pi-Stacking: A:F.66 pi-Cation interactions: A:H.134 01.5: 15 residues within 4Å: Chain A: L.184, L.189, V.192 Chain B: R.44, E.63, F.66, Q.114, I.116, A.133, H.134, I.177, V.178, F.179, F.180, V.210 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:E.63, B:V.178, B:F.180, B:V.210, A:L.184, A:L.189 Hydrogen bonds: B:V.178 Salt bridges: B:H.134 pi-Stacking: B:F.66, B:H.134

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain B: P.148, F.149, P.150 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, D. et al., Unraveling Small Molecule-Mediated Sirtuin 3 Activation at a Distinct Binding Site for Cardioprotective Therapies. Acs Cent.Sci. (2025)

Release Date

2025-06-25

Peptides

NAD-dependent protein deacetylase sirtuin-3, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

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