SMTL ID : 5yqm.1

Crystal structure of Sirt2 in complex with selective inhibitor A29

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 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

1 x A2X: 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-N-(4-phenylsulfanylphenyl)ethanamide(Non-covalent)

A2X.2: 24 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, F.185 Ligands: BME.4, BME.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.46, A:A.85, A:L.88, A:Y.89, A:Y.89, A:F.93, A:T.121, A:F.140, A:L.156, A:I.182 pi-Stacking: A:F.46, A:F.69, A:F.140, A:F.184

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

BME.3: 5 residues within 4Å: Chain A: Q.22, K.108, L.110, L.285, W.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.108, A:W.287 BME.4: 7 residues within 4Å: Chain A: F.46, R.47, F.69, V.183, F.184, F.185 Ligands: A2X.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.47 BME.5: 10 residues within 4Å: Chain A: G.34, A.35, I.43, D.45, F.46, Q.117, N.118, I.119, D.120 Ligands: A2X.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.118, A:I.119, A:D.120 BME.6: 9 residues within 4Å: Chain A: R.151, K.179, D.181, I.182, V.183, F.184, E.187, S.188, P.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.181

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

Related Entries With Identical Sequence