SMTL ID : 8ak9.2 (1 other biounit)

Human Sirt6 in complex with ADP-ribose and fragment Isatin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

PEG.1: 1 residues within 4Å: Chain A: Y.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.251, A:Y.251 PEG.4: 4 residues within 4Å: Chain A: T.78, T.79, F.80, E.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.80, A:E.81

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: 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: PG4.5 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.47, A:G.48, A:T.51, A:T.51, A:D.57, A:F.58, A:R.59, A:G.60, A:Q.107, A:T.209, A:S.210, A:N.234, A:L.235, A:Q.236, A:Q.236, A:V.252 Water bridges: A:T.51, A:L.211, A:L.211, A:L.211 Salt bridges: A:R.59, A:R.59, A:R.59

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 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)

PG4.5: 9 residues within 4Å: Chain A: W.65, L.180, D.181, W.182, D.184, L.186, I.213, R.214 Ligands: AR6.2 No protein-ligand interaction detected (PLIP)

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

SO4.6: 2 residues within 4Å: Chain A: H.62, K.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.75 Salt bridges: A:H.62 SO4.7: 4 residues within 4Å: Chain A: E.23, 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 SO4.8: 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 SO4.9: 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:V.147, A:G.149 Salt bridges: A:R.158 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:N.218 Salt bridges: A:R.214

1 x ISN: ISATIN(Non-covalent)

ISN.11: 9 residues within 4Å: Chain A: I.55, P.56, F.58, V.64, F.76, F.80, V.109, M.151 Ligands: CL.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.76, A:F.80

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

CL.12: 2 residues within 4Å: Chain A: W.65 Ligands: ISN.11 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
B

NAD-dependent protein deacetylase sirtuin-6

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