SMTL ID : 9fdu.1

Crystal structure of human Sirt2 in complex with a pyridine-3-carbothioamide-based fragment inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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 CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: T.210, S.211, L.212, Q.213 Ligand excluded by PLIP

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: K.237, A.238, G.239, Q.240 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.240, A:Q.240 Water bridges: A:G.239

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

EDO.4: 2 residues within 4Å: Chain A: A.33, D.43 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.43 EDO.5: 3 residues within 4Å: Chain A: Q.20, K.106, W.285 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.20, A:L.283 EDO.6: 6 residues within 4Å: Chain A: R.25, R.26, G.107, L.108, L.109, L.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.107

1 x 01: 6-[2,2,2-tris(fluoranyl)ethoxy]pyridine-3-carbothioamide

01.7: 11 residues within 4Å: Chain A: P.42, A.83, L.86, Y.87, P.88, F.91, F.138, L.154, M.157, K.158, I.161 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.87 Hydrogen bonds: A:P.42 pi-Stacking: A:F.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Friedrich, F. et al., Crystal structure of human Sirt2 in complex with a pyridine-3-carbothioamide-based fragment inhibitor. To Be Published

Release Date

2025-05-28

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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