SMTL ID : 8cno.1

Improved complex structure of human Sirtuin 6 with its inhibitor cis-resveratrol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 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: 24 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 Chain B: D.77 Ligands: STL.3, PG4.4 26 PLIP interactions: 25 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.47, A:G.48, A:T.51, A:T.51, A:D.57, A:F.58, A:R.59, A:R.59, A:G.60, A:H.127, A:S.210, A:N.234, A:L.235, A:Q.236, A:Q.236, A:V.252 Water bridges: A:T.51, A:Q.107, A:V.109, A:L.211, A:L.211, A:Q.212, A:D.253, B:K.75 Salt bridges: A:R.59, A:R.59 AR6.17: 25 residues within 4Å: Chain A: D.77 Chain B: G.46, A.47, G.48, T.51, D.57, F.58, R.59, W.65, Q.107, N.108, 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: STL.19, PGE.20 23 PLIP interactions: 22 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.47, B:G.48, B:T.51, B:D.57, B:F.58, B:R.59, B:R.59, B:T.209, B:S.210, B:N.234, B:L.235, B:Q.236, B:Q.236, B:V.252 Water bridges: B:T.51, B:Q.107, B:N.108, B:L.211, B:L.211, B:L.211, A:K.75 Salt bridges: B:R.59, B:R.59

2 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 ZN.18: 4 residues within 4Å: Chain B: C.135, C.138, C.160, C.171 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.135, B:C.138, B:C.160, B:C.171

2 x STL: RESVERATROL(Non-covalent)

STL.3: 13 residues within 4Å: Chain A: I.55, P.56, D.57, F.58, V.64, F.76, F.80, V.109, D.110, M.151, I.179 Ligands: AR6.1, PG4.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.55, A:F.58, A:F.76, A:F.80, A:V.109, A:V.109, A:I.179 Hydrogen bonds: A:P.56 Water bridges: A:V.109, A:D.110, A:D.110 STL.19: 13 residues within 4Å: Chain B: I.55, P.56, D.57, F.58, V.64, F.76, F.80, V.109, D.110, M.151, I.179 Ligands: AR6.17, PGE.20 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.55, B:F.58, B:F.58, B:F.76, B:F.80, B:V.109, B:V.109, B:I.179 Hydrogen bonds: B:P.56, B:D.110 Water bridges: B:V.109

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

PG4.4: 10 residues within 4Å: Chain A: W.65, L.180, D.181, W.182, D.184, L.186, I.213, R.214 Ligands: AR6.1, STL.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.186

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

EDO.5: 4 residues within 4Å: Chain A: Y.251 Chain B: F.76, T.79 Ligands: CL.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.251 EDO.21: 4 residues within 4Å: Chain B: A.279, L.280, P.281, P.282 No protein-ligand interaction detected (PLIP)

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

SO4.6: 4 residues within 4Å: Chain A: H.62, K.75 Chain B: H.62, K.75 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.75, A:K.75 Water bridges: B:K.75, A:K.75 Salt bridges: B:H.62, A:H.62 SO4.7: 3 residues within 4Å: Chain A: K.27, R.247, H.249 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.27, A:R.247 Salt bridges: A:K.27, A:R.247, A:H.249 SO4.8: 6 residues within 4Å: Chain A: R.84, A.269, W.270 Chain B: R.84, A.269, W.270 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.270, A:W.270, B:W.270 Water bridges: A:R.84, A:R.84 Salt bridges: A:R.84, B:R.84 SO4.9: 3 residues within 4Å: Chain A: R.199, R.225, R.226 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.199, A:R.225 SO4.10: 3 residues within 4Å: Chain A: R.214, P.215, N.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.214, A:N.218 SO4.11: 4 residues within 4Å: Chain A: V.148, G.149, T.156, R.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.149 Salt bridges: A:R.158 SO4.22: 4 residues within 4Å: Chain B: E.23, K.27, R.247, H.249 4 PLIP interactions: 4 interactions with chain B Water bridges: B:H.249 Salt bridges: B:K.27, B:R.247, B:H.249 SO4.23: 4 residues within 4Å: Chain B: V.148, G.149, T.156, R.158 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.147, B:G.149 Salt bridges: B:R.158 SO4.24: 3 residues within 4Å: Chain B: R.214, P.215, N.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.218 Salt bridges: B:R.214

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

CL.12: 3 residues within 4Å: Chain A: R.97, L.280, L.283 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: T.79, F.80, E.81 Ligands: PEG.16 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: L.72, A.73 Chain B: H.62 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: H.62 Chain B: A.73 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain B: P.74, K.75, F.76 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain B: T.79, F.80, E.81 Ligands: EDO.5 Ligand excluded by PLIP

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

PEG.16: 6 residues within 4Å: Chain A: F.76, T.78, T.79, F.80 Chain B: Y.251 Ligands: CL.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.251

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.20: 9 residues within 4Å: Chain B: L.180, D.181, W.182, D.184, L.186, I.213, R.214 Ligands: AR6.17, STL.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.182 Water bridges: B:D.184

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

2024-03-06

Peptides

NAD-dependent protein deacetylase sirtuin-6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-dependent protein deacetylase sirtuin-6

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