Research workbench
Crystal structure of SmyD3 in complex with covalent inhibitor 2
Analyse Crystal structure of SmyD3 in complex with covalent inhibitor 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XXG
- Type
- protein
- Length
- 423 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.14
- Source
- Homo sapiens
- Molecule
- SMYD3
- Ligands
- 8HR, SAM, ZN
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.14 · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SMYD3 | protein | 423 | 51% helix, 13% strand | — |
Ligands and binding sites
- 8HR · Propyl 4-(4-chloranyl-2-phenyl-quinolin-7-yl) carbonylpiperazine-1-carboxylate · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.79 | 0.81 | 84 | 8HR |
| 2 | 204 | 0.58 | 0.80 | 31 | SAM |
| 3 | 182 | 0.53 | 0.79 | 31 | empty |
| 4 | 114 | 0.43 | 0.77 | 27 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5XXG · Crystal structure of SMYD3 in complex with covalent inhibitor 2 · the same entry in another collection · 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
- Elsewhere: RCSB PDB 5XXG · PDBe 5XXG
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.