SMTL ID : 5yql.1

Crystal structure of Sirt2 in complex with selective inhibitor A2I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x A2I: 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-N-[3-(phenoxymethyl)phenyl]ethanamide(Non-covalent)

A2I.1: 21 residues within 4Å: Chain A: I.43, F.46, L.53, I.68, F.69, F.81, L.84, A.85, L.88, Y.89, P.90, F.93, I.119, D.120, T.121, F.140, L.156, I.163, I.182, V.183, F.184 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.69, A:F.81, A:F.81, A:L.84, A:L.88, A:Y.89, A:Y.89, A:F.93, A:F.140, A:L.156, A:I.182 Water bridges: A:F.46 pi-Stacking: A:F.140, A:F.184

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 8 residues within 4Å: Chain A: C.145, S.147, C.150, H.152, C.171, D.173, C.174, S.176 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.145, A:C.150, A:C.171, A:C.174

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.3: 3 residues within 4Å: Chain A: A.269, W.270, L.271 No protein-ligand interaction detected (PLIP) BME.4: 11 residues within 4Å: Chain A: G.34, A.35, G.36, D.45, R.47, Q.117, G.211, T.212, S.213, L.214, Q.215 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.211, A:S.213 Water bridges: A:S.213, A:N.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, L.L. et al., X-ray crystal structure guided discovery of new selective, substrate-mimicking sirtuin 2 inhibitors that exhibit activities against non-small cell lung cancer cells. Eur J Med Chem (2018)

Release Date

2018-10-17

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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