SMTL ID : 6p6g.1

Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 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)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: M.194, D.336, D.340, Y.362, V.375, Q.376, K.379 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.336 Water bridges: A:K.301 GOL.7: 7 residues within 4Å: Chain A: S.217, I.218, I.241, C.242, H.370, P.371 Ligands: LUP.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.217, A:I.218, A:C.242, A:C.242 GOL.8: 4 residues within 4Å: Chain A: P.103, Q.150, L.151, T.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.150, A:T.154 Water bridges: A:L.151

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.9: 15 residues within 4Å: Chain A: R.18, G.19, N.20, Y.128, E.134, N.136, N.185, S.206, L.207, L.208, N.209, H.210, Y.243, Y.261, F.263 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.20, A:N.20, A:N.20, A:N.20, A:E.134, A:N.136, A:N.209, A:H.210, A:H.210, A:Y.261 Water bridges: A:R.18, A:R.18, A:Y.128, A:Y.128, A:D.266 pi-Stacking: A:F.263, A:F.263

1 x LUP: 5-cyclopropyl-N-{1-[({trans-4-[(4,4,4-trifluorobutyl)amino]cyclohexyl}methyl)sulfonyl]piperidin-4-yl}-1,2-oxazole-3-carboxamide(Non-covalent)

LUP.10: 20 residues within 4Å: Chain A: C.184, N.185, S.186, F.187, T.188, C.190, M.194, E.196, S.206, I.241, Y.243, D.245, Y.261, L.294, E.298, K.333, C.337, H.370, V.372 Ligands: GOL.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.187, A:F.187, A:E.196, A:V.372 Hydrogen bonds: A:T.188, A:T.188, A:E.196, A:Y.243, A:D.245 Water bridges: A:Y.261 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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