SMTL ID : 7t1d.1

Human SIRT2 in complex with small molecule 359

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.140, C.145, C.166, C.169 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.140, A:C.145, A:C.166, A:C.169 ZN.8: 4 residues within 4Å: Chain B: C.140, C.145, C.166, C.169 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.140, B:C.145, B:C.166, B:C.169

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

SO4.2: 3 residues within 4Å: Chain A: R.23, L.107, K.198 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.23, A:K.198 SO4.3: 6 residues within 4Å: Chain A: G.29, A.30, R.42, Q.112, G.206, T.207 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.30, A:R.42, A:Q.112, A:T.207, A:S.208 Water bridges: A:G.31, A:G.31, A:H.132, A:Q.210 SO4.9: 3 residues within 4Å: Chain B: R.23, L.107, K.198 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.23 Salt bridges: B:R.23, B:K.198 SO4.10: 7 residues within 4Å: Chain B: G.29, A.30, R.42, Q.112, T.207, S.208, V.211 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:A.30, B:Q.112, B:G.206, B:S.208 Water bridges: B:G.31, B:G.31, B:R.42, B:R.42, B:R.42, B:V.211 Salt bridges: B:R.42

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

EDO.4: 5 residues within 4Å: Chain A: K.174, D.176, I.177, V.178, E.182 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.174 Water bridges: A:K.174, A:P.175, A:D.176, A:D.176 EDO.5: 5 residues within 4Å: Chain A: R.42, Q.112, H.132 Chain B: F.241 Ligands: E7K.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.112, A:H.132 EDO.11: 5 residues within 4Å: Chain B: K.174, D.176, I.177, V.178, E.182 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.174 Water bridges: B:H.139, B:K.174, B:D.176, B:D.176 EDO.12: 6 residues within 4Å: Chain A: Y.59, E.61 Chain B: K.234, A.235, G.236, Q.237 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.61, B:G.236, B:Q.237, B:Q.237 EDO.13: 5 residues within 4Å: Chain A: F.241 Chain B: Q.112, I.114, H.132 Ligands: E7K.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.132 Water bridges: B:R.42, B:Q.112 EDO.14: 4 residues within 4Å: Chain B: H.139, C.140, V.141, R.146 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.139, B:H.139 EDO.15: 5 residues within 4Å: Chain A: G.181 Chain B: Q.237, M.252, D.253, S.256 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.237, B:S.256, A:G.181 Water bridges: B:S.256

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

DMS.6: 2 residues within 4Å: Chain A: W.265, L.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.266 pi-Cation interactions: A:W.265 DMS.16: 3 residues within 4Å: Chain B: A.264, W.265, L.266 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.266 pi-Cation interactions: B:W.265

2 x E7K: 7-(2,4-dimethyl-1H-imidazol-1-yl)-2-(5-{[4-(1H-pyrazol-1-yl)phenyl]methyl}-1,3-thiazol-2-yl)-1,2,3,4-tetrahydroisoquinoline(Non-covalent)

E7K.7: 17 residues within 4Å: Chain A: F.41, R.42, F.64, F.76, A.80, Y.84, P.85, F.88, I.114, D.115, F.135, I.177, V.178, F.180, V.211 Chain B: F.241 Ligands: EDO.5 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.41, A:F.64, A:F.64, A:F.64, A:F.64, A:A.80, A:F.88, A:I.114, A:F.135, A:F.180, A:F.180, A:V.211, B:F.241, B:F.241 pi-Stacking: A:Y.84, A:F.135, B:F.241 E7K.17: 17 residues within 4Å: Chain A: F.241 Chain B: F.41, R.42, Y.49, F.64, F.76, A.80, Y.84, P.85, F.88, I.114, D.115, F.135, I.177, V.178, F.180 Ligands: EDO.13 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.41, B:R.42, B:F.64, B:F.64, B:F.64, B:F.64, B:A.80, B:Y.84, B:F.88, B:I.114, B:F.135, B:F.180, A:F.241 pi-Stacking: B:Y.84, B:F.135, A:F.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roche, K.L. et al., An allosteric inhibitor of sirtuin 2 deacetylase activity exhibits broad-spectrum antiviral activity. J.Clin.Invest. (2023)

Release Date

2023-05-17

Peptides

NAD-dependent protein deacetylase sirtuin-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-dependent protein deacetylase sirtuin-2