SMTL ID : 5mat.1

Structure of human Sirtuin 2 in complex with a selective thienopyrimidinone based inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 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 ZN.12: 8 residues within 4Å: Chain B: C.142, S.144, C.147, H.149, C.168, D.170, C.171, S.173 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.142, B:C.147, B:C.168, B:C.171

1 x 7KJ: (7~{R})-7-[(3,5-dimethyl-1,2-oxazol-4-yl)methylamino]-3-[(4-methoxynaphthalen-1-yl)methyl]-5,6,7,8-tetrahydro-[1]benzothiolo[2,3-d]pyrimidin-4-one(Non-covalent)

7KJ.2: 25 residues within 4Å: Chain A: I.40, P.41, F.43, Y.51, E.63, F.66, F.78, A.82, K.83, L.85, Y.86, P.87, F.90, I.116, D.117, T.118, F.137, L.153, K.157, I.160, F.161, I.179, V.180, F.181, F.182 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.43, A:F.43, A:F.43, A:F.66, A:F.66, A:A.82, A:Y.86, A:F.90, A:I.116, A:F.137, A:I.160 pi-Stacking: A:Y.86, A:F.137, A:F.137

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 8 residues within 4Å: Chain A: G.31, A.32, R.44, Q.114, T.209, S.210, L.211, V.213 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.32, A:Q.114, A:T.209, A:T.209, A:S.210 Water bridges: A:G.33, A:G.33, A:D.42, A:L.211, A:L.211, A:L.211, A:Q.212 SO4.4: 4 residues within 4Å: Chain A: A.237, G.238, Q.239, S.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.238, A:Q.239, A:Q.239, A:S.240 SO4.5: 4 residues within 4Å: Chain A: P.224, L.225, S.226, T.227 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.225, A:S.226, A:S.226 Water bridges: A:E.3 SO4.6: 2 residues within 4Å: Chain A: K.105, W.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.284 Salt bridges: A:K.105 SO4.7: 2 residues within 4Å: Chain A: K.236, Q.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.239 Water bridges: A:K.236 Salt bridges: A:K.236 SO4.8: 3 residues within 4Å: Chain A: R.148, P.187, A.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.188 SO4.9: 3 residues within 4Å: Chain A: R.25, L.109, K.200 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.25, A:R.25 Salt bridges: A:R.25, A:K.200 SO4.10: 6 residues within 4Å: Chain A: A.279, E.280, G.283, W.284, K.285, K.286 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.283, A:K.285, A:K.286 Water bridges: A:E.280, A:E.287 SO4.14: 4 residues within 4Å: Chain B: A.237, G.238, Q.239, S.240 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.238, B:Q.239, B:Q.239, B:S.240, B:S.240 Water bridges: B:S.240 SO4.15: 7 residues within 4Å: Chain B: A.279, E.280, G.283, W.284, K.285, K.286, E.287 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.283, B:G.283, B:K.285, B:K.286 Water bridges: B:E.287 SO4.16: 2 residues within 4Å: Chain B: S.258, K.259 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.259 Salt bridges: B:K.259 SO4.17: 2 residues within 4Å: Chain B: P.187, A.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.186, B:A.188 Water bridges: B:R.189 SO4.18: 7 residues within 4Å: Chain B: R.44, Q.114, T.209, S.210, L.211, Q.212, V.213 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.209, B:S.210, B:L.211, B:Q.212, B:V.213 Water bridges: B:Q.114, B:Q.114 SO4.19: 3 residues within 4Å: Chain B: R.25, L.109, K.200 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.200 Salt bridges: B:K.200

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.11: 6 residues within 4Å: Chain A: Q.273, L.276, A.277, E.280, K.285, E.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.285 Water bridges: A:E.289

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.13: 12 residues within 4Å: Chain B: S.221, K.222, A.223, P.224, L.225, R.229, G.249, L.250, G.251, G.252, Y.262, R.263 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.251, B:G.252, B:Y.262, B:R.263 Water bridges: B:R.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sundriyal, S. et al., Thienopyrimidinone Based Sirtuin-2 (SIRT2)-Selective Inhibitors Bind in the Ligand Induced Selectivity Pocket. J. Med. Chem. (2017)

Release Date

2017-02-08

Peptides

NAD-dependent protein deacetylase sirtuin-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

NAD-dependent protein deacetylase sirtuin-2

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