SMTL ID : 8owo.1

SMYD3 in complex with fragment FL01507

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

SAM.1: 20 residues within 4Å: Chain A: N.16, R.17, G.18, N.19, G.20, Y.127, L.132, E.133, N.135, C.183, N.184, S.205, L.206, L.207, N.208, H.209, Y.242, Y.260, C.261, F.262 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.17, A:N.19, A:N.19, A:N.19, A:Y.127, A:E.133, A:E.133, A:N.135, A:N.208, A:H.209, A:H.209, A:Y.260 Water bridges: A:R.17, A:R.17, A:R.17, A:E.133, A:K.138, A:D.265, A:D.265 pi-Stacking: A:F.262, A:F.262

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.211, R.252, C.264, C.266, R.268, 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.3: 6 residues within 4Å: Chain A: C.52, R.54, C.55, C.74, S.75, 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.4: 7 residues within 4Å: Chain A: C.65, Q.67, C.68, A.71, W.83, 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

1 x 9W9: 3-oxidanylbenzenecarbonitrile(Non-covalent)

9W9.5: 4 residues within 4Å: Chain A: P.102, Q.149, L.150, T.153 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.102, A:Q.149, A:L.150

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: C.183, N.184, S.185, F.186, S.205, I.240, Y.242, Q.259, Y.260 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.205, A:Y.260 Water bridges: A:S.185, A:Y.242, A:Y.242, A:Q.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

FitzGerald, E.A. et al., Identification of fragments targeting SMYD3 using highly sensitive kinetic and multiplexed biosensor-based screening. Rsc Med Chem (2024)

Release Date

2023-08-30

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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