Research workbench
X-ray structure of SMYD3 in complex with the benzodiazepine-based probe bay-6035
Analyse X-ray structure of SMYD3 in complex with the benzodiazepine-based probe bay-6035 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O2C
- Type
- protein
- Length
- 427 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SMYD3
- EC
- 2.1.1.354
- UniProt
- Q9H7B4
- Ligands
- UZK, SAM, ZN
- Pockets
- 4 · best druggability 0.79
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 2.1.1.354) | protein | 427 | 51% helix, 13% strand | Q9H7B4 |
Ligands and binding sites
- 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 · ligand · chains A
- SAM · S-adenosylmethionine · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · 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 | 1077 | 0.79 | 0.81 | 96 | UZK, SAM |
| 2 | 182 | 0.53 | 0.78 | 35 | empty |
| 3 | 104 | 0.44 | 0.78 | 25 | empty |
| 4 | 50 | 0.29 | 0.76 | 13 | empty |
Compared structures
- 7O2C · X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH the benzodiazepine-based probe BAY-6035 · 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 7O2C · PDBe 7O2C · UniProt Q9H7B4
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