SMTL ID : 9fdw.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x 01: 3-chloranyl-~{N}-(pyridin-2-ylmethyl)benzamide

01.1: 13 residues within 4Å: Chain A: F.44, F.67, F.79, L.82, A.83, L.86, Y.87, P.88, F.91, I.117, D.118, F.138 Ligands: 01.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.67, A:L.86, A:P.88, A:F.91, A:F.91, A:F.138, A:F.138 Water bridges: A:L.86 pi-Stacking: A:F.44, A:Y.87, A:F.138 Halogen bonds: A:F.79 01.2: 13 residues within 4Å: Chain A: R.45, F.67, I.117, H.135, I.180, V.181, F.182, F.183, E.185, L.187, V.214, Q.215 Ligands: 01.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.67, A:I.117, A:I.180, A:V.181, A:F.183, A:F.183, A:L.187 Hydrogen bonds: A:R.45, A:R.45, A:V.181 Water bridges: A:H.135

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: 3 residues within 4Å: Chain A: L.226, S.227, Y.263 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: A.267, W.268, L.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.268, A:L.269 Water bridges: A:A.267 EDO.6: 4 residues within 4Å: Chain A: M.19, Q.20, L.108, W.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.19

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Friedrich, F. et al., Crystal structure of human Sirt2 in complex with a 3-chlorobenzamide-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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