SMTL ID : 6paf.1

Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.212, C.265, C.267, C.270 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.212, A:C.265, A:C.267, A:C.270 ZN.2: 4 residues within 4Å: Chain A: C.66, C.69, H.87, C.91 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.69, A:H.87, A:C.91 ZN.3: 4 residues within 4Å: Chain A: C.53, C.56, C.75, C.79 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.53, A:C.56, A:C.75, A:C.79

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: E.193, M.194, K.301, D.336, D.340, Y.362, V.372, V.375, Q.376, K.379 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.301, A:K.301, A:D.336 GOL.7: 7 residues within 4Å: Chain A: S.217, I.218, I.241, C.242, H.370, P.371 Ligands: O6A.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.218, A:C.242 Water bridges: A:L.244, A:H.370

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

SAM.8: 17 residues within 4Å: Chain A: R.18, G.19, N.20, Y.128, E.134, N.136, C.184, N.185, S.206, L.207, L.208, N.209, H.210, Y.243, Y.261, F.263 Ligands: O6A.9 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.20, A:N.20, A:N.20, A:E.134, A:N.136, A:N.209, A:N.209, A:H.210, A:H.210, A:Y.261 Water bridges: A:R.18, A:Y.128, A:Y.128, A:D.266, A:D.266 pi-Stacking: A:F.263, A:F.263

1 x O6A: N-(1-{[4-(aminomethyl)phenyl]sulfonyl}piperidin-4-yl)-5-cyclopropyl-1,2-oxazole-3-carboxamide(Non-covalent)

O6A.9: 17 residues within 4Å: Chain A: C.184, N.185, S.186, F.187, T.188, C.190, M.194, I.241, C.242, Y.243, L.244, D.245, Y.261, H.370, V.372 Ligands: GOL.7, SAM.8 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.187, A:F.187, A:Y.243, A:Y.261, A:V.372 Hydrogen bonds: A:T.188, A:K.301, A:K.301 Water bridges: A:C.242, A:M.246, A:Y.261, A:E.298, A:E.298 pi-Stacking: A:F.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, D.S. et al., Discovery of Isoxazole Amides as Potent and Selective SMYD3 Inhibitors. Acs Med.Chem.Lett. (2020)

Release Date

2020-01-15

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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