Research workbench
Crystal structure of SMYD3 with SAM and oxindole compound
Analyse Crystal structure of SMYD3 with SAM and oxindole compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CCL
- Type
- protein
- Length
- 425 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SMYD3
- EC
- 2.1.1.43
- UniProt
- Q9H7B4
- Ligands
- 4ZW, SAM, ZN
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SMYD3 (EC 2.1.1.43) | protein | 425 | 51% helix, 13% strand | Q9H7B4 |
Ligands and binding sites
- 4ZW · 2-oxidanylidene-N-piperidin-4-yl-1,3-dihydroindole-5-carboxamide · ligand · 2 copies · chains A
- SAM · S-adenosylmethionine · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.80 | 0.81 | 94 | SAM, 4ZW |
| 2 | 174 | 0.54 | 0.79 | 25 | empty |
| 3 | 112 | 0.44 | 0.78 | 27 | empty |
| 4 | 64 | 0.30 | 0.74 | 12 | empty |
Compared structures
- 5CCL · Crystal structure of SMYD3 with SAM and oxindole compound · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H7B4 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SMYD3 (Q9H7B4) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q9H7B4
- Elsewhere: RCSB PDB 5CCL · PDBe 5CCL · UniProt Q9H7B4
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