SMTL ID : 9g7h.1

Human Sirt6 in complex with ADP-ribose and the inhibitor 2-Pr

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-hexamer

Ligands

6 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: 23 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: 01.3 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.47, A:G.48, A:T.51, A:T.51, A:F.58, A:R.59, A:R.59, A:G.60, A:W.65, 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:L.211, A:L.211, B:K.75, B:K.75 Salt bridges: A:R.59, A:R.59 AR6.9: 22 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, H.127, W.182, G.208, T.209, S.210, I.213, N.234, L.235, Q.236, G.250, Y.251, V.252 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:A.47, B:T.51, B:F.58, B:R.59, B:R.59, B:Q.107, 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:L.211 Salt bridges: B:R.59, B:R.59 AR6.13: 23 residues within 4Å: Chain C: 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 D: D.77 Ligands: 01.15 23 PLIP interactions: 21 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:A.47, C:G.48, C:T.51, C:T.51, C:F.58, C:R.59, C:R.59, C:G.60, C:W.65, C:H.127, C:S.210, C:N.234, C:L.235, C:Q.236, C:Q.236, C:V.252 Water bridges: C:T.51, C:L.211, C:L.211, D:K.75, D:K.75 Salt bridges: C:R.59, C:R.59 AR6.21: 22 residues within 4Å: Chain C: D.77 Chain D: 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 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:A.47, D:T.51, D:F.58, D:R.59, D:R.59, D:Q.107, D:T.209, D:S.210, D:N.234, D:L.235, D:Q.236, D:Q.236, D:V.252 Water bridges: D:T.51, D:L.211 Salt bridges: D:R.59, D:R.59 AR6.25: 23 residues within 4Å: Chain E: 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 F: D.77 Ligands: 01.27 23 PLIP interactions: 21 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:A.47, E:G.48, E:T.51, E:T.51, E:F.58, E:R.59, E:R.59, E:G.60, E:W.65, E:H.127, E:S.210, E:N.234, E:L.235, E:Q.236, E:Q.236, E:V.252 Water bridges: E:T.51, E:L.211, E:L.211, F:K.75, F:K.75 Salt bridges: E:R.59, E:R.59 AR6.33: 22 residues within 4Å: Chain E: D.77 Chain F: 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 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:A.47, F:T.51, F:F.58, F:R.59, F:R.59, F:Q.107, F:T.209, F:S.210, F:N.234, F:L.235, F:Q.236, F:Q.236, F:V.252 Water bridges: F:T.51, F:L.211 Salt bridges: F:R.59, F:R.59

6 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.10: 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 ZN.14: 4 residues within 4Å: Chain C: C.135, C.138, C.160, C.171 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.135, C:C.138, C:C.160, C:C.171 ZN.22: 4 residues within 4Å: Chain D: C.135, C.138, C.160, C.171 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.135, D:C.138, D:C.160, D:C.171 ZN.26: 4 residues within 4Å: Chain E: C.135, C.138, C.160, C.171 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.135, E:C.138, E:C.160, E:C.171 ZN.34: 4 residues within 4Å: Chain F: C.135, C.138, C.160, C.171 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.135, F:C.138, F:C.160, F:C.171

3 x 01: 2,4-bis(oxidanylidene)-1-[2-oxidanylidene-2-[[(2S)-3-oxidanylidene-3-(propylamino)-2-[3-(3-pyridin-3-yl-1,2,4-oxadiazol-5-yl)propanoylamino]propyl]amino]ethyl]pyrimidine-5-carboxamide

01.3: 15 residues within 4Å: Chain A: I.55, P.56, F.58, F.76, T.78, T.79, F.80, V.109, H.127, M.130, M.151, I.179, L.180, W.182 Ligands: AR6.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.58, A:F.58, A:V.109, A:I.179, A:L.180 Hydrogen bonds: A:T.78, A:L.180 pi-Stacking: A:F.80, A:W.182 01.15: 15 residues within 4Å: Chain C: I.55, P.56, F.58, F.76, T.78, T.79, F.80, V.109, H.127, M.130, M.151, I.179, L.180, W.182 Ligands: AR6.13 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.58, C:F.58, C:V.109, C:I.179, C:L.180 Hydrogen bonds: C:T.78, C:L.180 pi-Stacking: C:F.80, C:W.182 01.27: 15 residues within 4Å: Chain E: I.55, P.56, F.58, F.76, T.78, T.79, F.80, V.109, H.127, M.130, M.151, I.179, L.180, W.182 Ligands: AR6.25 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:F.58, E:F.58, E:V.109, E:I.179, E:L.180 Hydrogen bonds: E:T.78, E:L.180 pi-Stacking: E:F.80, E:W.182

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

SO4.4: 5 residues within 4Å: Chain A: H.62, K.75, D.77 Chain B: H.62, K.75 Ligand excluded by PLIP SO4.5: 6 residues within 4Å: Chain A: R.84, A.269, W.270 Chain B: R.84, A.269, W.270 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: K.27, R.247, H.249 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: P.215, N.218 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: G.152, L.153, R.176 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: K.27, R.247, H.249 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: R.214, P.215, N.218 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain C: H.62, K.75, D.77 Chain D: H.62, K.75 Ligand excluded by PLIP SO4.17: 6 residues within 4Å: Chain C: R.84, A.269, W.270 Chain D: R.84, A.269, W.270 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: K.27, R.247, H.249 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain C: P.215, N.218 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain C: G.152, L.153, R.176 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain D: K.27, R.247, H.249 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain D: R.214, P.215, N.218 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain E: H.62, K.75, D.77 Chain F: H.62, K.75 Ligand excluded by PLIP SO4.29: 6 residues within 4Å: Chain E: R.84, A.269, W.270 Chain F: R.84, A.269, W.270 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain E: K.27, R.247, H.249 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain E: P.215, N.218 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain E: G.152, L.153, R.176 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain F: K.27, R.247, H.249 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain F: R.214, P.215, N.218 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

You, W. et al., Elucidating the Unconventional Binding Mode of a DNA-Encoded Library Hit Provides a Blueprint for Sirtuin 6 Inhibitor Development. Chemmedchem (2024)

Release Date

2024-08-14

Peptides

NAD-dependent protein deacetylase sirtuin-6: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

NAD-dependent protein deacetylase sirtuin-6

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