SMTL ID : 7qnu.1

SMYD3 in complex with fragment FL08619

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 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, 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, C.264 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:N.19, A:N.19, A:N.19, A:N.19, A:Y.127, 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:E.133, A:K.138, 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: H.209, C.211, R.252, 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.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 173: BENZOYL-FORMIC ACID(Non-covalent)

173.5: 7 residues within 4Å: Chain A: L.7, L.32, L.33, F.34, R.35, E.122, K.125 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.7, A:R.35 Water bridges: A:R.35 Salt bridges: A:K.8 pi-Stacking: A:F.34

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

2023-04-05

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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