SMTL ID : 8py3.1

Crystal structure of human Sirt2 in complex with a 1,2,4-oxadiazole based inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 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 I1R: 4-chloranyl-~{N}-[4-[5-[[(3~{S})-1-[(3-fluoranyl-2-methyl-phenyl)methyl]piperidin-3-yl]methyl]-1,2,4-oxadiazol-3-yl]phenyl]benzamide(Non-covalent)

I1R.2: 14 residues within 4Å: Chain A: F.44, L.51, F.67, L.86, Y.87, P.88, F.91, D.118, F.138, V.181, F.182, F.183, E.185, L.187 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.44, A:F.44, A:F.67, A:P.88, A:F.91, A:F.138, A:F.138, A:V.181, A:F.183, A:F.183, A:F.183, A:L.187 Hydrogen bonds: A:V.181 pi-Stacking: A:F.67, A:Y.87, A:F.138

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

BTB.3: 6 residues within 4Å: Chain A: K.73, K.74, P.76, E.77, K.168, L.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.77, A:K.168 Salt bridges: A:E.77

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

EDO.4: 3 residues within 4Å: Chain A: A.278, E.281, L.282 No protein-ligand interaction detected (PLIP) EDO.5: 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.6: 3 residues within 4Å: Chain A: E.290, D.291, R.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.291 Water bridges: A:R.295 EDO.7: 2 residues within 4Å: Chain A: Q.115, H.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.115, A:H.135 EDO.8: 4 residues within 4Å: Chain A: K.177, D.179, I.180, E.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.177 Water bridges: A:K.177, A:P.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Colcerasa, A. et al., Structure-Activity Studies of 1,2,4-Oxadiazoles for the Inhibition of the NAD + -Dependent Lysine Deacylase Sirtuin 2. J.Med.Chem. (2024)

Release Date

2024-06-19

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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