SMTL ID : 5y2f.1

Human SIRT6 in complex with allosteric activator MDL-801

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

monomer

Ligands

1 x THR- ALA- ARG- LYS- SER- THR- GLY- GLY: 9-mer peptide QTARKSTGG(Non-covalent)

THR-ALA-ARG-LYS-SER-THR-GLY-GLY.1: 17 residues within 4Å: Chain A: D.12, L.184, D.185, W.186, E.187, D.188, S.189, L.190, D.192, Q.216, I.217, R.218, P.219 Ligands: AR6.2, PEG.16, HDR.17, SO4.18 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.190, A:I.217, A:I.217 Hydrogen bonds: A:D.12, A:D.12, A:E.187, A:E.187, A:D.188, A:S.189, A:S.189, A:L.190, A:R.218, A:R.218 Water bridges: A:H.131, A:S.189

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: 24 residues within 4Å: Chain A: E.20, G.50, A.51, G.52, T.55, D.61, F.62, R.63, W.69, Q.111, H.131, G.212, T.213, S.214, I.217, N.238, L.239, Q.240, G.254, Y.255, V.256 Ligands: THR-ALA-ARG-LYS-SER-THR-GLY-GLY.1, SO4.13, HDR.17 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:E.20, A:E.20, A:A.51, A:T.55, A:T.55, A:F.62, A:R.63, A:R.63, A:Q.111, A:T.213, A:S.214, A:L.215, A:N.238, A:L.239, A:Q.240, A:Q.240, A:V.256 Water bridges: A:T.55, A:R.63, A:I.217 Salt bridges: A:R.63, A:R.63

1 x 8L9: 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid(Non-covalent)

8L9.3: 12 residues within 4Å: Chain A: N.2, A.5, E.72, P.78, F.80, T.83, F.84, E.85, M.134, V.151 Ligands: GOL.9, HDR.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.78, A:F.84, A:F.84 Hydrogen bonds: A:N.2, A:F.84

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.139, C.142, C.164, C.175 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.139, A:C.142, A:C.164, A:C.175

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: K.243, H.244, R.246, H.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.243 Water bridges: A:R.246 GOL.6: 3 residues within 4Å: Chain A: R.124, Q.145, E.281 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.124, A:E.281 Water bridges: A:Q.145, A:V.147 GOL.7: 2 residues within 4Å: Chain A: K.228, H.247 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.228 GOL.8: 4 residues within 4Å: Chain A: E.34, R.37, Q.41, R.233 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.34, A:Q.41, A:R.233, A:R.233 Water bridges: A:E.34 GOL.9: 7 residues within 4Å: Chain A: A.5, M.134, V.151, G.153, T.154, M.155 Ligands: 8L9.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.153, A:T.154 Water bridges: A:A.5, A:M.155

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

SO4.10: 1 residues within 4Å: Chain A: R.180 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.180 SO4.11: 4 residues within 4Å: Chain A: T.154, A.159, T.160, G.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.159 SO4.12: 4 residues within 4Å: Chain A: R.218, P.219, N.222 Ligands: PEG.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.218, A:N.222 SO4.13: 5 residues within 4Å: Chain A: E.20, T.55, L.239, Y.255 Ligands: AR6.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.55 Water bridges: A:E.20, A:D.61, A:D.61 SO4.14: 4 residues within 4Å: Chain A: D.23, K.31, R.251, H.253 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.31, A:R.251, A:H.253 SO4.15: 2 residues within 4Å: Chain A: W.33, K.265 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.265, A:H.266 SO4.18: 4 residues within 4Å: Chain A: R.218 Ligands: THR-ALA-ARG-LYS-SER-THR-GLY-GLY.1, THR-ALA-ARG-LYS-SER-THR-GLY-GLY.1, THR-ALA-ARG-LYS-SER-THR-GLY-GLY.1 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.16: 6 residues within 4Å: Chain A: L.195, D.199, N.222, L.223 Ligands: THR-ALA-ARG-LYS-SER-THR-GLY-GLY.1, SO4.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.222

1 x HDR: HEXADECANE-1-SULFINIC ACID(Non-covalent)

HDR.17: 11 residues within 4Å: Chain A: L.7, P.60, F.80, T.82, F.84, M.155, L.184, W.186 Ligands: THR-ALA-ARG-LYS-SER-THR-GLY-GLY.1, AR6.2, 8L9.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.7, A:F.80, A:F.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Z. et al., Identification of a cellularly active SIRT6 allosteric activator. Nat. Chem. Biol. (2018)

Release Date

2018-11-07

Peptides

NAD-dependent protein deacetylase sirtuin-6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-6

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