MolNFT v1 · #145027 · protein
Crystal structure of human set and mynd domain containing protein 2 with MTF1497
6CBX · N-lysine methyltransferase SMYD2: “Crystal structure of human set and mynd domain containing protein 2 with MTF1497”. X-ray diffraction, 4 ligands (EW1, ZN, UNX), 9 pockets (best druggability 0.79). MolNFT v1 #145027 on GenesisL1…
- PDB
- 6CBX
- Type
- protein
- Length
- 861 residues
- Chains
- 2
- 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
- EW1, ZN, UNX, CL
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 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 | 428 | 52% helix, 14% strand | Q9NRG4 |
| B | N-lysine methyltransferase SMYD2 (EC 2.1.1.-, 2.1.1.43) | protein | 433 | 50% helix, 14% strand | Q9NRG4 |
Ligands and binding sites
- EW1 · [3-(4-amino-6-methyl-1H-imidazo[4,5-c]pyridin-1-yl) azetidin-1-yl][1-({1-[(1R)-cyclohept-2-en-1-yl]piperidin-4-yl}methyl)-1H-pyrrol-3-yl]methanone · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- UNX · Unknown atom or ion · ion · 10 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.79 | 0.81 | 89 | EW1, CL, UNX |
| 2 | 1023 | 0.78 | 0.79 | 99 | EW1, CL, EDO, UNX |
| 3 | 375 | 0.63 | 0.78 | 29 | empty |
| 4 | 222 | 0.52 | 0.76 | 39 | UNX |
| 5 | 106 | 0.39 | 0.75 | 18 | UNX |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6CBX · Crystal structure of human SET and MYND Domain Containing protein 2 with MTF1497 · 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 6CBX · PDBe 6CBX · UniProt Q9NRG4
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