MolNFT v1 · #138233 · protein
Set and mynd domain containing protein 2
5WCG · N-lysine methyltransferase SMYD2: “Set and mynd domain containing protein 2”. X-ray diffraction, 3 ligands (A4M, ZN, UNX), 5 pockets (best druggability 0.78). MolNFT v1 #138233 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5WCG
- Type
- protein
- Length
- 430 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
- A4M, ZN, UNX
- Pockets
- 5 · best druggability 0.78
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 | 430 | 51% helix, 14% strand | Q9NRG4 |
Ligands and binding sites
- A4M · [3-(6-amino-2-methyl-9H-purin-9-yl)azetidin-1-yl]{5-[(4-cycloheptylpiperazin-1-yl)methyl]-1-methyl-1H-pyrazol-3-yl}methanone · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- UNX · Unknown atom or ion · ion · 5 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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 | 961 | 0.78 | 0.80 | 87 | A4M, UNX |
| 2 | 91 | 0.38 | 0.76 | 18 | DMS |
| 3 | 65 | 0.38 | 0.79 | 15 | empty |
| 4 | 110 | 0.36 | 0.73 | 19 | empty |
| 5 | 53 | 0.29 | 0.75 | 11 | empty |
Compared structures
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 5WCG · PDBe 5WCG · UniProt Q9NRG4
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