SMTL ID : 4i5i.3 (2 other biounits)

Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x 4I5: (6S)-2-chloro-5,6,7,8,9,10-hexahydrocyclohepta[b]indole-6-carboxamide(Non-covalent)

4I5.1: 16 residues within 4Å: Chain A: A.25, I.33, P.34, F.36, I.42, F.60, I.79, Q.108, N.109, I.110, D.111, H.126, I.174, V.175, F.176 Ligands: NAD.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.25, A:I.33, A:F.36, A:I.42, A:I.79, A:I.110, A:I.110, A:I.110, A:H.126 Hydrogen bonds: A:S.28, A:Q.108, A:I.110, A:D.111, A:D.111 pi-Stacking: A:F.36 4I5.4: 15 residues within 4Å: Chain B: A.25, I.33, P.34, F.36, I.42, F.60, Q.108, N.109, I.110, D.111, H.126, I.174, V.175, F.176 Ligands: NAD.5 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.25, B:I.33, B:F.36, B:F.36, B:I.42, B:I.110, B:I.110, B:I.110, B:H.126 Hydrogen bonds: B:Q.108, B:I.110, B:D.111, B:D.111 pi-Stacking: B:F.36, B:F.60

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 25 residues within 4Å: Chain A: G.24, A.25, G.26, V.29, D.35, F.36, R.37, Y.43, Q.57, F.60, Q.108, H.126, V.175, F.177, G.203, S.204, S.205, V.208, N.228, R.229, E.230, G.243, D.244, C.245 Ligands: 4I5.1 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:F.60 Hydrogen bonds: A:A.25, A:G.26, A:D.35, A:F.36, A:R.37, A:R.37, A:R.37, A:Y.43, A:F.60, A:F.60, A:Q.108, A:Q.108, A:S.205, A:L.206, A:N.228, A:R.229, A:R.229, A:E.230, A:E.230, A:D.244, A:C.245 Water bridges: A:V.29, A:S.38 Salt bridges: A:R.37, A:R.37 pi-Stacking: A:F.177 pi-Cation interactions: A:R.229 NAD.5: 25 residues within 4Å: Chain B: G.24, A.25, G.26, V.29, D.35, F.36, R.37, Y.43, Q.57, F.60, Q.108, H.126, V.175, F.177, G.203, S.204, S.205, V.208, N.228, R.229, E.230, G.243, D.244, C.245 Ligands: 4I5.4 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:F.60 Hydrogen bonds: B:A.25, B:G.26, B:D.35, B:F.36, B:R.37, B:R.37, B:R.37, B:Y.43, B:Q.57, B:F.60, B:Q.108, B:Q.108, B:S.204, B:S.205, B:L.206, B:N.228, B:R.229, B:R.229, B:E.230, B:E.230, B:D.244, B:C.245 Water bridges: B:V.29, B:S.38 Salt bridges: B:R.37, B:R.37 pi-Stacking: B:F.177 pi-Cation interactions: B:R.229

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.134, C.137, C.158, C.161 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.134, A:C.137, A:C.158, A:C.161 ZN.6: 4 residues within 4Å: Chain B: C.134, C.137, C.158, C.161 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.134, B:C.137, B:C.158, B:C.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, X. et al., The 2.5 angstrom crystal structure of the SIRT1 catalytic domain bound to nicotinamide adenine dinucleotide (NAD+) and an indole (EX527 analogue) reveals a novel mechanism of histone deacetylase inhibition. J.Med.Chem. (2013)

Release Date

2013-01-23

Peptides

NAD-dependent protein deacetylase sirtuin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-dependent protein deacetylase sirtuin-1

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