SMTL ID : 5mar.1 (1 other biounit)

Structure of human SIRT2 in complex with 1,2,4-Oxadiazole inhibitor and ADP ribose.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: C.142, S.144, C.147, H.149, C.168, D.170, C.171, S.173 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.142, A:C.147, A:C.168, A:C.171

1 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Non-covalent)

AR6.2: 26 residues within 4Å: Chain A: G.31, A.32, G.33, T.36, S.37, D.42, F.43, R.44, S.45, Y.51, Q.114, H.134, F.182, G.208, T.209, S.210, L.211, V.213, N.233, K.234, E.235, G.269, E.270, C.271 Ligands: 7KE.3, EDO.5 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:A.32, A:G.33, A:F.43, A:R.44, A:R.44, A:Y.51, A:Q.114, A:Q.114, A:H.134, A:T.209, A:S.210, A:S.210, A:L.211, A:N.233, A:N.233, A:K.234, A:K.234, A:E.235, A:E.270, A:C.271 Water bridges: A:S.37, A:S.45, A:E.270, A:D.272 Salt bridges: A:R.44, A:R.44

1 x 7KE: 3-[3-(4-chlorophenyl)-1,2,4-oxadiazol-5-yl]propan-1-ol(Non-covalent)

7KE.3: 15 residues within 4Å: Chain A: P.41, F.43, L.50, F.66, F.78, L.81, A.82, L.85, I.116, H.134, I.179, V.180, F.181 Ligands: AR6.2, DMS.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.50, A:L.81, A:L.81, A:L.85, A:L.85, A:I.116, A:I.179

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

EDO.4: 6 residues within 4Å: Chain A: L.9, F.256, D.257, S.258, K.259, A.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.257 Water bridges: A:K.259 EDO.5: 5 residues within 4Å: Chain A: T.36, S.37, K.234, E.270 Ligands: AR6.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.234

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

DMS.6: 3 residues within 4Å: Chain A: A.266, W.267, L.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.268 pi-Cation interactions: A:W.267 DMS.7: 9 residues within 4Å: Chain A: A.32, S.35, I.40, P.41, F.43, N.115, I.116, D.117 Ligands: 7KE.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.116, A:D.117 Salt bridges: A:D.117 DMS.8: 7 residues within 4Å: Chain A: R.24, R.25, G.106, L.107, L.108, L.109 Ligands: DMS.9 No protein-ligand interaction detected (PLIP) DMS.9: 6 residues within 4Å: Chain A: L.108, L.109, R.110, E.128, D.129 Ligands: DMS.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.129 DMS.10: 4 residues within 4Å: Chain A: Y.51, D.52, E.55, P.62 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.52

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 12 residues within 4Å: Chain A: G.238, Q.239, S.240, D.241, P.242, M.246, M.248, G.249, L.250, G.251, G.252, G.253 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.238, A:S.240, A:G.251, A:G.253 GOL.12: 6 residues within 4Å: Chain A: R.100, I.122, G.124, E.295, S.298, I.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.100, A:S.298, A:S.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moniot, S. et al., Development of 1,2,4-Oxadiazoles as Potent and Selective Inhibitors of the Human Deacetylase Sirtuin 2: Structure-Activity Relationship, X-ray Crystal Structure, and Anticancer Activity. J. Med. Chem. (2017)

Release Date

2017-03-15

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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