SMTL ID : 8qoo.1

Crystal structure of human Sirt2 in complex with the peptide-based pseudo-inhibitor TNFn-4.1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-1-mer

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 BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.2: 2 residues within 4Å: Chain A: K.73, K.74 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.74

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

EDO.3: 3 residues within 4Å: Chain A: A.267, W.268, L.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.267, A:L.269 Water bridges: A:L.269

1 x WH8: (2S,3S)-3-dodecylsulfanyl-2-methyl-butanoic acid(Non-covalent)

WH8.4: 16 residues within 4Å: Chain A: F.44, R.45, L.51, F.67, A.83, L.86, Y.87, P.88, F.91, I.117, D.118, H.135, F.138, V.181 Chain B: K.6 Ligands: WGN.5 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.44, A:L.51, A:F.67, A:F.67, A:L.86, A:L.86, A:Y.87, A:Y.87, A:P.88, A:F.91, A:I.117, A:D.118, A:H.135, A:F.138, A:F.138, A:F.138, A:F.138, B:K.6 Hydrogen bonds: A:R.45 Water bridges: A:H.135

1 x WGN: (2S,3R)-3-dodecylsulfanyl-2-methyl-butanoic acid(Non-covalent)

WGN.5: 16 residues within 4Å: Chain A: F.44, R.45, F.67, F.79, A.83, L.86, Y.87, P.88, I.117, D.118, H.135, F.138, V.181, F.183 Chain B: K.6 Ligands: WH8.4 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.44, A:F.44, A:F.67, A:F.67, A:F.79, A:L.86, A:Y.87, A:P.88, A:I.117, A:I.117, A:D.118, A:F.138, A:F.138, A:F.138, A:F.183, B:K.6 Hydrogen bonds: A:R.45 Water bridges: A:H.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Friedrich, F. et al., Development of potent TNFa-Myr-based pseudo-inhibitors for Sirtuin 2. To Be Published

Release Date

2024-10-09

Peptides

NAD-dependent protein deacetylase sirtuin-2: A
Peptide-based pseudo-inhibitor TNFn-4.1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-dependent protein deacetylase sirtuin-2

Peptide-based pseudo-inhibitor TNFn-4.1

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