SMTL ID : 6zrb.1

Crystal structure of SMYD3 conjugate with piperidine-based covalent inhibitor EM127

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 17 residues within 4Å: Chain A: R.17, G.18, N.19, Y.127, E.133, N.135, C.183, N.184, S.205, L.206, L.207, N.208, H.209, Y.242, Y.260, F.262 Ligands: QON.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.19, A:N.19, A:N.19, A:Y.127, A:E.133, A:N.135, A:N.135, A:N.208, A:N.208, A:H.209, A:H.209, A:Y.242 Water bridges: A:R.17, A:E.133, A:E.133, A:D.265, A:D.265 pi-Stacking: A:F.262, A:F.262

1 x QON: N-[1-(2-Chloroacetyl)piperidin-4-yl]-5-cyclopropyl-1,2-oxazole-3-carboxamide(Covalent)

QON.2: 13 residues within 4Å: Chain A: C.183, N.184, S.185, F.186, T.187, C.189, M.193, I.217, F.219, I.240, Y.242, Y.260 Ligands: SAM.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.186, A:F.186, A:I.217, A:F.219, A:Y.242, A:Y.260 Hydrogen bonds: A:T.187 Water bridges: A:C.241, A:Y.242 pi-Stacking: A:F.186

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: P.102, Q.149, T.153 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.150

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.211, C.264, C.266, C.269 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.211, A:C.264, A:C.266, A:C.269 ZN.5: 4 residues within 4Å: Chain A: C.52, C.55, C.74, C.78 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.52, A:C.55, A:C.74, A:C.78 ZN.6: 4 residues within 4Å: Chain A: C.65, C.68, H.86, C.90 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.65, A:C.68, A:H.86, A:C.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parenti, M.D. et al., Discovery of the 4-aminopiperidine-based compound EM127 for the site-specific covalent inhibition of SMYD3. Eur.J.Med.Chem. (2022)

Release Date

2022-07-27

Peptides

Histone-lysine N-methyltransferase SMYD3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SMYD3

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