SMTL ID : 8bl1.1 (1 other biounit)

Human Sirt6 in complex with the inhibitor S6039 and ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

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)

AR6.1: 22 residues within 4Å: Chain A: G.46, A.47, G.48, T.51, D.57, F.58, R.59, W.65, Q.107, H.127, W.182, G.208, T.209, S.210, I.213, N.234, L.235, Q.236, G.250, Y.251, V.252 Ligands: QY3.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:A.47, A:G.48, A:T.51, A:T.51, A:F.58, A:R.59, A:Q.107, A:H.127, A:S.210, A:N.234, A:L.235, A:Q.236, A:Q.236, A:V.252 Salt bridges: A:R.59, A:R.59, A:R.59

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.135, C.138, C.160, C.171 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.135, A:C.138, A:C.160, A:C.171

1 x QY3: 2-azanyl-5-[4-[[5-(2-fluorophenyl)thiophen-2-yl]methyl]piperazin-1-yl]sulfonyl-benzenesulfonamide(Non-covalent)

QY3.3: 20 residues within 4Å: Chain A: A.47, S.50, I.55, P.56, D.57, F.58, V.64, F.80, N.108, V.109, D.110, H.127, M.130, M.151, L.180, D.181, W.182, I.213 Ligands: AR6.1, CL.9 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.58, A:V.64, A:F.80, A:V.109, A:L.180, A:I.213 Hydrogen bonds: A:P.56, A:V.109, A:D.110, A:D.110, A:D.110 pi-Stacking: A:H.127, A:W.182, A:W.182

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

PEG.4: 6 residues within 4Å: Chain A: F.76, T.78, T.79, F.80, E.81 Ligands: CL.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.80, A:E.81, A:E.81

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

SO4.5: 3 residues within 4Å: Chain A: K.27, R.247, H.249 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.27, A:R.247, A:H.249 SO4.6: 3 residues within 4Å: Chain A: R.84, A.269, W.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.270 Salt bridges: A:R.84 SO4.7: 3 residues within 4Å: Chain A: R.214, P.215, N.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.218 SO4.8: 3 residues within 4Å: Chain A: V.148, G.149, R.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.149 Salt bridges: A:R.158

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 3 residues within 4Å: Chain A: F.80 Ligands: QY3.3, PEG.4 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: R.97, L.280, L.283 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

You, W. et al., Development of novel Sirtuin 6 inhibitors and activators based on a protein crystallography-based fragment screen. To Be Published

Release Date

2023-11-22

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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