Research workbench
Crystal structure of protein lysine methyltransferase SMYD2 in complex with lly-507, a cell-active, potent and selective inhibitor
Analyse Crystal structure of protein lysine methyltransferase SMYD2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WUY
- Type
- protein
- Length
- 414 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-lysine methyltransferase SMYD2
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9NRG4
- Ligands
- 3UJ, SAH, ZN
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-lysine methyltransferase SMYD2 (EC 2.1.1.-, 2.1.1.43) | protein | 414 | 52% helix, 14% strand | Q9NRG4 |
Ligands and binding sites
- 3UJ · 5-cyano-2'-{4-[2-(3-methyl-1H-indol-1-yl)ethyl]piperazin-1-yl}-N-[3-(pyrrolidin-1-yl)propyl]biphenyl-3-carboxamide · ligand · chains A
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- ZN · Zinc ion · metal · 4 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.79 | 0.81 | 101 | 3UJ, SAH, GOL |
| 2 | 59 | 0.41 | 0.81 | 14 | empty |
| 3 | 86 | 0.36 | 0.76 | 17 | GOL |
Compared structures
- 4WUY · Crystal Structure of Protein Lysine Methyltransferase SMYD2 in complex with LLY-507, a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NRG4 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase SMYD2 (Q9NRG4) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9NRG4
- Elsewhere: RCSB PDB 4WUY · PDBe 4WUY · UniProt Q9NRG4
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