SMTL ID : 7o2c.1

X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH the benzodiazepine-based probe BAY-6035

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

1 x UZK: (2S)-1-[[(1R,5S)-3-azabicyclo[3.1.0]hexan-3-yl]carbonyl]-N-(2-cyclopropylethyl)-2-methyl-4-oxidanylidene-3,5-dihydro-2H-1,5-benzodiazepine-7-carboxamide(Non-covalent)

UZK.1: 13 residues within 4Å: Chain A: C.180, S.182, F.183, T.184, C.186, M.190, I.214, F.216, Y.239, Y.257, H.366, V.368 Ligands: SAM.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.183, A:F.183, A:T.184, A:Y.239, A:Y.239, A:Y.239, A:Y.257, A:V.368 Hydrogen bonds: A:T.184, A:T.184, A:C.186, A:Y.239

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

SAM.2: 17 residues within 4Å: Chain A: R.14, G.15, N.16, Y.124, E.130, N.132, C.180, N.181, S.202, L.203, L.204, N.205, H.206, Y.239, Y.257, F.259 Ligands: UZK.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.16, A:N.16, A:E.130, A:N.132, A:N.132, A:N.205, A:N.205, A:H.206, A:H.206 Water bridges: A:R.14, A:R.14, A:R.14, A:R.14, A:Y.124, A:Y.124 pi-Stacking: A:F.259, A:F.259

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.208, C.261, C.263, C.266 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.208, A:C.261, A:C.263, A:C.266 ZN.4: 4 residues within 4Å: Chain A: C.49, C.52, C.71, C.75 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.49, A:C.52, A:C.71, A:C.75 ZN.5: 4 residues within 4Å: Chain A: C.62, C.65, H.83, C.87 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.62, A:C.65, A:H.83, A:C.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gradl, S. et al., Discovery of the SMYD3 Inhibitor BAY-6035 Using Thermal Shift Assay (TSA)-Based High-Throughput Screening. Slas Discov (2021)

Release Date

2021-07-07

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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