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

Human Sirt6 in complex with ADP-ribose and fragment 4-amino-6-chlorobenzene-1,3-disulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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: 21 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, G.208, T.209, S.210, I.213, N.234, L.235, Q.236, G.250, Y.251, V.252 Ligands: PG4.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.47, A:T.51, A:T.51, A:F.58, A:R.59, A:G.60, A:Q.107, A:H.127, A:S.210, A:L.211, A:N.234, A:L.235, A:Q.236, A:Q.236, A:V.252 Water bridges: A:T.51, A:Q.212, A:D.253 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 PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 10 residues within 4Å: Chain A: W.65, H.127, L.180, D.181, W.182, D.184, L.186, I.213, R.214 Ligands: AR6.1 No protein-ligand interaction detected (PLIP)

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

EDO.4: 4 residues within 4Å: Chain A: F.80, M.130 Ligands: I7B.13, CL.14 No protein-ligand interaction detected (PLIP)

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

PEG.5: 1 residues within 4Å: Chain A: Y.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.251

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

SO4.6: 2 residues within 4Å: Chain A: H.62, K.75 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.75 Water bridges: A:H.62, A:K.75, A:D.77, A:D.77 Salt bridges: 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: 3 residues within 4Å: Chain A: R.84, A.269, W.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.270 Water bridges: A:R.84 Salt bridges: A:R.84 SO4.9: 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 SO4.10: 5 residues within 4Å: Chain A: V.147, V.148, G.149, T.156, R.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.149 Water bridges: A:R.158 Salt bridges: A:R.158 SO4.11: 2 residues within 4Å: Chain A: K.224, H.243 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.224, A:H.243 SO4.12: 3 residues within 4Å: Chain A: P.61, H.62, R.70 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.62, A:R.70

1 x I7B: 4-AMINO-6-CHLOROBENZENE-1,3-DISULFONAMIDE(Non-covalent)

I7B.13: 15 residues within 4Å: Chain A: A.47, S.50, I.55, P.56, D.57, F.58, V.64, F.76, F.80, N.108, V.109, D.110, M.130, M.151 Ligands: EDO.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.64, A:F.80, A:V.109 Hydrogen bonds: A:P.56, A:V.109, A:D.110, A:D.110 Water bridges: A:A.47, A:A.47, A:P.56 pi-Stacking: A:F.58

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

CL.14: 4 residues within 4Å: Chain A: T.79, F.80, E.81 Ligands: EDO.4 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

2023-08-16

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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