SMTL ID : 7cl1.1

Human SIRT6 in complex with allosteric activator MDL-801 (3.2A)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

1 x THR- ALA- ARG- LYS- SER- THR- GLY- GLY: THR-ALA-ARG-LYS-SER-THR-GLY-GLY(Non-covalent)

THR-ALA-ARG-LYS-SER-THR-GLY-GLY.1: 16 residues within 4Å: Chain A: D.14, H.133, L.186, W.188, E.189, D.190, S.191, L.192, L.197, Q.218, I.219, R.220, P.221 Ligands: AR6.2, G4X.11, SO4.12 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.186, A:L.192, A:L.197, A:I.219, A:I.219 Hydrogen bonds: A:D.14, A:D.14, A:E.189, A:E.189, A:D.190, A:S.191, A:L.192, A:R.220, A:R.220 Water bridges: A:R.220, A:R.220

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: 23 residues within 4Å: Chain A: E.22, G.52, A.53, G.54, T.57, D.63, F.64, R.65, W.71, Q.113, H.133, G.214, T.215, S.216, I.219, N.240, L.241, Q.242, G.256, Y.257, V.258 Ligands: THR-ALA-ARG-LYS-SER-THR-GLY-GLY.1, G4X.11 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:E.22, A:E.22, A:A.53, A:T.57, A:T.57, A:F.64, A:R.65, A:G.66, A:Q.113, A:T.215, A:S.216, A:L.217, A:N.240, A:L.241, A:Q.242, A:Q.242, A:V.258 Salt bridges: A:R.65, A:R.65, A:R.65

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.141, C.144, C.166, C.177 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.141, A:C.144, A:C.166, A:C.177

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

8L9.4: 12 residues within 4Å: Chain A: N.4, A.6, A.7, F.82, T.85, F.86, E.87, M.136, V.153, M.157 Ligands: GOL.8, G4X.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.86, A:F.86 Hydrogen bonds: A:N.4, A:F.86

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 1 residues within 4Å: Chain A: R.284 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.284 GOL.6: 4 residues within 4Å: Chain A: W.35, K.267, H.268, P.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.267, A:K.267 GOL.7: 5 residues within 4Å: Chain A: L.159, L.186, S.191, L.192, P.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.184 GOL.8: 7 residues within 4Å: Chain A: A.7, M.136, V.153, G.155, T.156, M.157 Ligands: 8L9.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.155, A:T.156 Water bridges: A:T.156

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

SO4.9: 4 residues within 4Å: Chain A: R.220, P.221, N.224 Ligands: PEG.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.220, A:N.224 SO4.12: 3 residues within 4Å: 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.10: 3 residues within 4Å: Chain A: D.201, L.225 Ligands: SO4.9 No protein-ligand interaction detected (PLIP)

1 x G4X: hexadecanethial(Non-covalent)

G4X.11: 17 residues within 4Å: Chain A: L.9, I.61, P.62, F.64, V.70, F.82, F.86, N.114, V.115, D.116, M.157, L.186, D.187, W.188 Ligands: THR-ALA-ARG-LYS-SER-THR-GLY-GLY.1, AR6.2, 8L9.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.9, A:I.61, A:F.64, A:F.64, A:F.64, A:V.70, A:F.82, A:F.86, A:N.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Z. et al., Reply to: Binding site for MDL-801 on SIRT6. Nat.Chem.Biol. (2021)

Release Date

2021-02-24

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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