SMTL ID : 9fru.1

Crystal structure of human Sirt2 in complex with a pyrazole-based fragment inhibitor and NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.143, C.148, C.169, C.172 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.143, A:C.148, A:C.169, A:C.172

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: L.226, S.227, Y.263 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.4 EDO.4: 3 residues within 4Å: Chain A: A.267, W.268, L.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.267, A:L.269

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: K.237, A.238, G.239, Q.240 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.240, A:Q.240 Water bridges: A:G.239

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

NAD.5: 23 residues within 4Å: Chain A: G.32, A.33, G.34, T.37, I.41, P.42, D.43, F.44, R.45, Q.115, N.116, I.117, D.118, H.135, G.209, T.210, S.211, N.234, K.235, E.236, G.270, E.271, C.272 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:A.33, A:D.43 Hydrogen bonds: A:A.33, A:T.37, A:T.37, A:Q.115, A:I.117, A:D.118, A:D.118, A:D.118, A:H.135, A:T.210, A:T.210, A:S.211, A:S.211, A:N.234, A:K.235, A:C.272 Water bridges: A:S.38, A:L.212, A:L.212, A:D.273 pi-Stacking: A:F.44 pi-Cation interactions: A:K.235

1 x 01: [2-[2-methyl-5-(trifluoromethyl)pyrazol-3-yl]phenyl]methanol

01.6: 14 residues within 4Å: Chain A: I.41, F.44, F.67, F.79, L.82, A.83, L.86, Y.87, P.88, F.91, I.117, D.118, F.138, I.180 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.41, A:P.88, A:F.91, A:I.117, A:D.118, A:F.138, A:F.138 Halogen bonds: A:F.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Friedrich, F. et al., Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand Interactions. J.Med.Chem. (2025)

Release Date

2025-06-04

Peptides

NAD-dependent protein deacetylase sirtuin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-2

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