SMTL ID : 9fds.1

Crystal structure of human Sirt2 in complex with SirReal2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 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

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

DMS.3: 5 residues within 4Å: Chain A: K.237, A.238, G.239, Q.240, S.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.240, A:Q.240 Water bridges: A:G.239 DMS.5: 3 residues within 4Å: Chain A: L.226, S.227, Y.263 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.4

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

EDO.4: 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 EDO.6: 5 residues within 4Å: Chain A: R.45, F.67, V.181, F.183 Ligands: 3TE.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.45, A:R.45, A:V.181 EDO.7: 4 residues within 4Å: Chain A: Q.20, K.106, L.108, W.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.20

1 x 3TE: 2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]-N-[5-(naphthalen-1-ylmethyl)-1,3-thiazol-2-yl]acetamide(Non-covalent)

3TE.8: 19 residues within 4Å: Chain A: I.41, F.44, Y.52, I.66, F.67, F.79, A.83, L.86, Y.87, P.88, F.91, I.117, D.118, F.138, L.154, I.180, V.181, F.182 Ligands: EDO.6 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.44, A:F.44, A:F.67, A:F.67, A:F.79, A:A.83, A:Y.87, A:Y.87, A:F.91, A:I.117, A:F.138, A:F.138, A:L.154, A:I.180 pi-Stacking: A:F.138, A:F.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Friedrich, F. et al., Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand Interactions. J.Med.Chem. (2025)

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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