SMTL ID : 8owz.1

Crystal structure of human Sirt2 in complex with a triazole-based SirReal

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x KZU: 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-N-[5-[[3-[[1-(2-methoxyethyl)-1,2,3-triazol-4-yl]methoxy]phenyl]methyl]-1,3-thiazol-2-yl]ethanamide(Non-covalent)

KZU.1: 21 residues within 4Å: Chain A: I.41, F.44, R.45, F.67, F.79, L.82, A.83, L.86, Y.87, P.88, F.91, I.117, D.118, H.135, F.138, L.154, I.180, V.181, F.182, F.183 Ligands: BU3.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.44, A:F.67, A:F.67, A:F.79, A:L.82, A:A.83, A:Y.87, A:Y.87, A:F.91, A:F.138, A:F.138, A:L.154, A:I.180 Hydrogen bonds: A:R.45 pi-Stacking: A:F.44, A:F.138, A:F.182

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: E.290, D.291, R.294 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.294 Water bridges: A:E.290, A:E.290, A:E.290, A:D.291, A:R.295 EDO.6: 3 residues within 4Å: Chain A: A.267, W.268, L.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.267, A:L.269 EDO.7: 3 residues within 4Å: Chain A: L.226, Y.263, R.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.263, A:Y.263, A:R.264 Water bridges: A:R.230 EDO.8: 1 residues within 4Å: Chain A: R.122 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.122

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.3: 8 residues within 4Å: Chain A: K.73, K.74, P.76, E.77, T.166, K.168, L.175 Ligands: BU3.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.77, A:K.168

2 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.4: 3 residues within 4Å: Chain A: K.73, K.74 Ligands: BTB.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.74 BU3.5: 11 residues within 4Å: Chain A: A.33, I.41, P.42, D.43, F.44, R.45, Q.115, N.116, I.117, D.118 Ligands: KZU.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.33, A:I.41, A:I.117 Hydrogen bonds: A:R.45, A:R.45, A:N.116, A:I.117, A:D.118, A:D.118

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 4 residues within 4Å: Chain A: C.143, C.148, C.169, C.172 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.143, A:C.148, A:C.169, A:C.172

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 5 residues within 4Å: Chain A: Q.115, T.210, L.212, Q.213, V.214 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sinatra, L. et al., Development of First-in-Class Dual Sirt2/HDAC6 Inhibitors as Molecular Tools for Dual Inhibition of Tubulin Deacetylation. J.Med.Chem. (2023)

Release Date

2023-11-15

Peptides

NAD-dependent protein deacetylase sirtuin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-2

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