SMTL ID : 9fdx.1

Crystal structure of human Sirt2 in complex with the peptide-based inhibitor KT9

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

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

DMS.2: 7 residues within 4Å: Chain A: R.45, Q.115, T.210, S.211, L.212, Q.213, V.214 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.115, A:T.210, A:L.212, A:Q.213, A:V.214 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.4: 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

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

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:W.268, A:L.269 EDO.7: 1 residues within 4Å: Chain A: H.59 No protein-ligand interaction detected (PLIP)

1 x 01: (2~{S})-2-acetamido-~{N}-[(2~{S},3~{R})-1-azanyl-3-oxidanyl-1-oxidanylidene-butan-2-yl]-6-[[(3~{R})-3-(3,4-dichlorophenyl)sulfanylbutanoyl]amino]hexanamide

01.6: 16 residues within 4Å: Chain A: F.44, R.45, F.67, F.79, Q.115, I.117, H.135, I.180, V.181, F.182, F.183, E.185, L.187, V.214, Q.215, P.216 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.135, A:F.183 Hydrogen bonds: A:R.45, A:Q.215, A:Q.215 Water bridges: A:H.135, A:E.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Friedrich, F. et al., Crystal structure of human Sirt2 in complex with the peptide-based inhibitor KT9. 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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