SMTL ID : 8i2b.1

Human SIRT6 in complex with inhibitor 7702

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

PG4.1: 10 residues within 4Å: Chain A: H.125, M.149, L.178, D.179, W.180, L.184, I.211, R.212 Ligands: O5L.2, AR6.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.212 PG4.5: 5 residues within 4Å: Chain A: F.74, T.76, T.77 Chain B: F.16, Y.249 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.249 PG4.6: 6 residues within 4Å: Chain B: L.178, D.179, W.180, D.182, L.184 Ligands: AR6.8 No protein-ligand interaction detected (PLIP) PG4.15: 10 residues within 4Å: Chain C: H.125, M.149, L.178, D.179, W.180, L.184, I.211, R.212 Ligands: O5L.16, AR6.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.212 PG4.19: 5 residues within 4Å: Chain C: F.74, T.76, T.77 Chain D: F.16, Y.249 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.249 PG4.20: 6 residues within 4Å: Chain D: L.178, D.179, W.180, D.182, L.184 Ligands: AR6.22 No protein-ligand interaction detected (PLIP) PG4.29: 10 residues within 4Å: Chain E: H.125, M.149, L.178, D.179, W.180, L.184, I.211, R.212 Ligands: O5L.30, AR6.31 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.212 PG4.33: 5 residues within 4Å: Chain E: F.74, T.76, T.77 Chain F: F.16, Y.249 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.249 PG4.34: 6 residues within 4Å: Chain F: L.178, D.179, W.180, D.182, L.184 Ligands: AR6.36 No protein-ligand interaction detected (PLIP)

6 x O5L: N1-[[4-(4-aminophenyl)sulfanyl-3-(trifluoromethyl)phenyl]methoxy]benzene-1,4-dicarboxamide

O5L.2: 13 residues within 4Å: Chain A: A.45, S.48, I.53, P.54, F.56, V.62, W.63, F.74, F.78, N.106, V.107, D.108 Ligands: PG4.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.53, A:F.56, A:F.56, A:F.78, A:V.107 Hydrogen bonds: A:S.48, A:S.48, A:V.107, A:D.108, A:D.108 Water bridges: A:A.45 O5L.7: 13 residues within 4Å: Chain B: A.45, I.53, P.54, D.55, F.56, V.62, W.63, E.66, F.74, F.78, V.107, D.108, M.149 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.53, B:F.56, B:V.62, B:F.74, B:F.78, B:V.107 Hydrogen bonds: B:D.108 Halogen bonds: B:E.66 O5L.16: 13 residues within 4Å: Chain C: A.45, S.48, I.53, P.54, F.56, V.62, W.63, F.74, F.78, N.106, V.107, D.108 Ligands: PG4.15 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.53, C:F.56, C:F.56, C:F.78, C:V.107 Hydrogen bonds: C:S.48, C:S.48, C:V.107, C:D.108, C:D.108 Water bridges: C:A.45 O5L.21: 13 residues within 4Å: Chain D: A.45, I.53, P.54, D.55, F.56, V.62, W.63, E.66, F.74, F.78, V.107, D.108, M.149 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.53, D:F.56, D:V.62, D:F.74, D:F.78, D:V.107 Hydrogen bonds: D:D.108 Halogen bonds: D:E.66 O5L.30: 13 residues within 4Å: Chain E: A.45, S.48, I.53, P.54, F.56, V.62, W.63, F.74, F.78, N.106, V.107, D.108 Ligands: PG4.29 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:I.53, E:F.56, E:F.56, E:F.78, E:V.107 Hydrogen bonds: E:S.48, E:S.48, E:V.107, E:D.108, E:D.108 Water bridges: E:A.45 O5L.35: 13 residues within 4Å: Chain F: A.45, I.53, P.54, D.55, F.56, V.62, W.63, E.66, F.74, F.78, V.107, D.108, M.149 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.53, F:F.56, F:V.62, F:F.74, F:F.78, F:V.107 Hydrogen bonds: F:D.108 Halogen bonds: F:E.66

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)

AR6.3: 23 residues within 4Å: Chain A: G.44, A.45, G.46, T.49, D.55, F.56, R.57, W.63, Q.105, H.125, W.180, G.206, T.207, S.208, I.211, N.232, L.233, Q.234, G.248, Y.249, V.250 Chain B: D.75 Ligands: PG4.1 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:A.45, A:G.46, A:T.49, A:T.49, A:D.55, A:F.56, A:R.57, A:G.58, A:Q.105, A:H.125, A:T.207, A:S.208, A:N.232, A:L.233, A:Q.234, A:Q.234, A:V.250 Salt bridges: A:R.57, A:R.57, A:R.57 AR6.8: 23 residues within 4Å: Chain A: D.75 Chain B: G.44, A.45, G.46, T.49, D.55, F.56, R.57, W.63, Q.105, H.125, W.180, G.206, T.207, S.208, I.211, N.232, L.233, Q.234, G.248, Y.249, V.250 Ligands: PG4.6 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:A.45, B:G.46, B:T.49, B:F.56, B:R.57, B:R.57, B:T.207, B:S.208, B:L.209, B:N.232, B:L.233, B:Q.234, B:Q.234, B:V.250 Salt bridges: B:R.57, B:R.57 AR6.17: 23 residues within 4Å: Chain C: G.44, A.45, G.46, T.49, D.55, F.56, R.57, W.63, Q.105, H.125, W.180, G.206, T.207, S.208, I.211, N.232, L.233, Q.234, G.248, Y.249, V.250 Chain D: D.75 Ligands: PG4.15 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:A.45, C:G.46, C:T.49, C:T.49, C:D.55, C:F.56, C:R.57, C:G.58, C:Q.105, C:H.125, C:T.207, C:S.208, C:N.232, C:L.233, C:Q.234, C:Q.234, C:V.250 Salt bridges: C:R.57, C:R.57, C:R.57 AR6.22: 23 residues within 4Å: Chain C: D.75 Chain D: G.44, A.45, G.46, T.49, D.55, F.56, R.57, W.63, Q.105, H.125, W.180, G.206, T.207, S.208, I.211, N.232, L.233, Q.234, G.248, Y.249, V.250 Ligands: PG4.20 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:A.45, D:G.46, D:T.49, D:F.56, D:R.57, D:R.57, D:T.207, D:S.208, D:L.209, D:N.232, D:L.233, D:Q.234, D:Q.234, D:V.250 Salt bridges: D:R.57, D:R.57 AR6.31: 23 residues within 4Å: Chain E: G.44, A.45, G.46, T.49, D.55, F.56, R.57, W.63, Q.105, H.125, W.180, G.206, T.207, S.208, I.211, N.232, L.233, Q.234, G.248, Y.249, V.250 Chain F: D.75 Ligands: PG4.29 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:A.45, E:G.46, E:T.49, E:T.49, E:D.55, E:F.56, E:R.57, E:G.58, E:Q.105, E:H.125, E:T.207, E:S.208, E:N.232, E:L.233, E:Q.234, E:Q.234, E:V.250 Salt bridges: E:R.57, E:R.57, E:R.57 AR6.36: 23 residues within 4Å: Chain E: D.75 Chain F: G.44, A.45, G.46, T.49, D.55, F.56, R.57, W.63, Q.105, H.125, W.180, G.206, T.207, S.208, I.211, N.232, L.233, Q.234, G.248, Y.249, V.250 Ligands: PG4.34 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:A.45, F:G.46, F:T.49, F:F.56, F:R.57, F:R.57, F:T.207, F:S.208, F:L.209, F:N.232, F:L.233, F:Q.234, F:Q.234, F:V.250 Salt bridges: F:R.57, F:R.57

6 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.133, C.136, C.158, C.169 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.133, A:C.136, A:C.158, A:C.169 ZN.9: 5 residues within 4Å: Chain B: C.133, K.135, C.136, C.158, C.169 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.133, B:C.136, B:C.158, B:C.169 ZN.18: 4 residues within 4Å: Chain C: C.133, C.136, C.158, C.169 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.133, C:C.136, C:C.158, C:C.169 ZN.23: 5 residues within 4Å: Chain D: C.133, K.135, C.136, C.158, C.169 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.133, D:C.136, D:C.158, D:C.169 ZN.32: 4 residues within 4Å: Chain E: C.133, C.136, C.158, C.169 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.133, E:C.136, E:C.158, E:C.169 ZN.37: 5 residues within 4Å: Chain F: C.133, K.135, C.136, C.158, C.169 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.133, F:C.136, F:C.158, F:C.169

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

SO4.10: 4 residues within 4Å: Chain A: H.60, K.73 Chain B: H.60, K.73 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:H.60, A:K.73 Salt bridges: A:H.60, B:H.60 SO4.11: 4 residues within 4Å: Chain B: E.21, K.25, R.245, H.247 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.25, B:R.245, B:H.247 SO4.12: 7 residues within 4Å: Chain A: R.82, A.267, W.268 Chain B: R.82, P.266, A.267, W.268 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:P.266, B:W.268, A:W.268 Salt bridges: B:R.82, A:R.82 SO4.13: 3 residues within 4Å: Chain B: R.197, R.223, R.224 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.197, B:R.223, B:R.224 SO4.14: 3 residues within 4Å: Chain B: R.212, P.213, N.216 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.216 Salt bridges: B:R.212 SO4.24: 4 residues within 4Å: Chain C: H.60, K.73 Chain D: H.60, K.73 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Salt bridges: D:H.60, C:H.60 Water bridges: C:H.60, C:K.73 SO4.25: 4 residues within 4Å: Chain D: E.21, K.25, R.245, H.247 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:K.25, D:R.245, D:H.247 SO4.26: 7 residues within 4Å: Chain C: R.82, A.267, W.268 Chain D: R.82, P.266, A.267, W.268 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:P.266, D:W.268, C:W.268 Salt bridges: D:R.82, C:R.82 SO4.27: 3 residues within 4Å: Chain D: R.197, R.223, R.224 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:R.197, D:R.223, D:R.224 SO4.28: 3 residues within 4Å: Chain D: R.212, P.213, N.216 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.216 Salt bridges: D:R.212 SO4.38: 4 residues within 4Å: Chain E: H.60, K.73 Chain F: H.60, K.73 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Water bridges: E:H.60, E:K.73 Salt bridges: E:H.60, F:H.60 SO4.39: 4 residues within 4Å: Chain F: E.21, K.25, R.245, H.247 3 PLIP interactions: 3 interactions with chain F Salt bridges: F:K.25, F:R.245, F:H.247 SO4.40: 7 residues within 4Å: Chain E: R.82, A.267, W.268 Chain F: R.82, P.266, A.267, W.268 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:P.266, F:W.268, E:W.268 Salt bridges: F:R.82, E:R.82 SO4.41: 3 residues within 4Å: Chain F: R.197, R.223, R.224 3 PLIP interactions: 3 interactions with chain F Salt bridges: F:R.197, F:R.223, F:R.224 SO4.42: 3 residues within 4Å: Chain F: R.212, P.213, N.216 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.216 Salt bridges: F:R.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y., The SIRT6 in complex with inhibitor 7702. To Be Published

Release Date

2024-01-17

Peptides

NAD-dependent protein deacylase 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 deacylase sirtuin-6