MolNFT v1 · #78379 · protein
Structural basis of substrate methylation and inhibition of SMYD2
3S7B · N-lysine methyltransferase SMYD2: “Structural basis of substrate methylation and inhibition of SMYD2”. X-ray diffraction, 3 ligands (SAM, NH5, ZN), 5 pockets (best druggability 0.77). MolNFT v1 #78379 on GenesisL1: 3D structure…
- PDB
- 3S7B
- Type
- protein
- Length
- 429 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
- SAM, NH5, ZN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 51% 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 | 429 | 51% helix, 14% strand | Q9NRG4 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- NH5 · N-cyclohexyl-N~3~-[2-(3,4-dichlorophenyl)ethyl]-N-(2-{[2-(5-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-8-yl)ethyl]amino}ethyl)-beta-alaninamide · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- BU3 · (R,R)-2,3-butanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.77 | 0.79 | 95 | SAM, NH5 |
| 2 | 110 | 0.40 | 0.75 | 19 | BU3 |
| 3 | 56 | 0.38 | 0.80 | 15 | empty |
| 4 | 56 | 0.30 | 0.75 | 14 | empty |
| 5 | 61 | 0.27 | 0.73 | 13 | empty |
Compared structures
- 3S7B · Structural Basis of Substrate Methylation and Inhibition of SMYD2 · 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 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 Q9NRG4
- Elsewhere: RCSB PDB 3S7B · PDBe 3S7B · UniProt Q9NRG4
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