SMTL ID : 6nr0.1 (1 other biounit)

SIRT2(56-356) with covalent intermediate between mechanism-based inhibitor Glucose-TM-1beta and 1'-SH ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.158, C.163, H.165, C.184, C.187, S.189 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.158, A:C.163, A:C.184, A:C.187 ZN.8: 5 residues within 4Å: Chain B: C.158, C.163, C.184, C.187, S.189 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.158, B:C.163, B:C.184, B:C.187

2 x KXJ: N~2~-[3-(2-hydroxyethoxy)propanoyl]-N-phenyl-N~6~-tetradecanethioyl-L-lysinamide(Non-covalent)

KXJ.2: 24 residues within 4Å: Chain A: F.59, F.82, F.94, L.97, A.98, L.101, Y.102, P.103, F.106, I.132, D.133, H.150, I.195, V.196, F.197, F.198, G.199, E.200, S.201, L.202, V.229, Q.230, P.231 Ligands: KXG.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.82, A:F.82, A:L.97, A:L.101, A:F.106, A:I.132, A:I.195, A:V.196, A:F.198 Hydrogen bonds: A:V.196, A:G.199, A:E.200, A:Q.230 KXJ.9: 20 residues within 4Å: Chain B: F.59, L.66, F.82, F.94, L.97, L.101, I.132, H.150, I.195, V.196, F.197, F.198, G.199, E.200, S.201, L.202, V.229, Q.230, P.231 Ligands: KXG.10 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.82, B:F.82, B:F.94, B:L.97, B:L.101, B:F.198, B:V.229 Hydrogen bonds: B:V.196, B:G.199, B:E.200, B:Q.230

2 x KXG: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-sulfanyl-oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

KXG.3: 28 residues within 4Å: Chain A: G.47, A.48, G.49, T.52, S.53, D.58, F.59, R.60, S.61, F.82, Q.130, H.150, F.198, G.224, T.225, S.226, L.227, V.229, I.248, N.249, K.250, E.251, A.253, G.285, E.286, C.287 Ligands: KXJ.2, NA.4 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:A.48, A:G.49, A:T.52, A:F.59, A:R.60, A:R.60, A:R.60, A:Q.130, A:H.150, A:H.150, A:G.224, A:T.225, A:T.225, A:S.226, A:S.226, A:N.249, A:K.250, A:E.286, A:C.287 Water bridges: A:S.53, A:S.61, A:E.251 Salt bridges: A:R.60, A:R.60 KXG.10: 26 residues within 4Å: Chain B: G.47, A.48, G.49, T.52, S.53, D.58, F.59, R.60, S.61, Q.130, H.150, F.198, G.224, T.225, S.226, L.227, V.229, N.249, K.250, E.251, G.285, E.286, C.287 Ligands: KXJ.9, NA.11, NA.12 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:A.48, B:T.52, B:D.58, B:F.59, B:R.60, B:R.60, B:R.60, B:S.61, B:Q.130, B:H.150, B:T.225, B:S.226, B:S.226, B:N.249, B:K.250, B:E.251, B:E.251, B:E.286, B:C.287 Water bridges: B:S.53, B:D.288 Salt bridges: B:R.60, B:R.60

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: S.226, E.251 Ligands: KXG.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.60, A:E.251 NA.5: 3 residues within 4Å: Chain A: R.245, G.269, D.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.269 Water bridges: A:R.279 NA.11: 6 residues within 4Å: Chain B: G.47, A.48, F.59, Q.130, N.131 Ligands: KXG.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.48, B:Q.130 NA.12: 5 residues within 4Å: Chain B: R.60, S.61, S.226, E.251 Ligands: KXG.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.60

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

SO4.6: 3 residues within 4Å: Chain A: R.41, L.125, K.216 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.41, A:K.216 SO4.13: 7 residues within 4Å: Chain A: K.252, Q.255, D.273 Chain B: R.60, Y.67, E.79, Q.228 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.255, A:D.273, B:Y.67, B:E.79, B:E.79, B:Q.228 Water bridges: A:K.252 Salt bridges: B:R.60

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: A.282, W.283, L.284 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.284 GOL.14: 3 residues within 4Å: Chain B: A.282, W.283, L.284 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.284 GOL.15: 3 residues within 4Å: Chain A: Q.230 Chain B: S.256, G.265 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.256 GOL.16: 5 residues within 4Å: Chain B: E.296, G.299, W.300, K.301, K.302 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.296, B:E.296, B:K.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, J.Y. et al., A Glycoconjugated SIRT2 Inhibitor with Aqueous Solubility Allows Structure-Based Design of SIRT2 Inhibitors. Acs Chem.Biol. (2019)

Release Date

2020-01-22

Peptides

NAD-dependent protein deacetylase sirtuin-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-dependent protein deacetylase sirtuin-2

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