MolNFT v1 · #79226 · protein
Crystal structure of DOT1L in complex with a brominated sah analog
3SX0 · Histone-lysine N-methyltransferase, H3 lysine-79 specific: “Crystal structure of DOT1L in complex with a brominated sah analog”. X-ray diffraction, 3 ligands (SX0, UNX, SO4), 3 pockets (best druggability 0.69). MolNFT v1 #79226 on…
- PDB
- 3SX0
- Type
- protein
- Length
- 324 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-79 specific
- EC
- 2.1.1.43
- UniProt
- Q8TEK3
- Ligands
- SX0, UNX, SO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 324 | 42% helix, 15% strand | Q8TEK3 |
Ligands and binding sites
- SX0 · (2S)-2-amino-4-({[(2S,3S,4R,5R)-5-(4-amino-5-bromo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred name) · ligand · chains A
- UNX · Unknown atom or ion · ion · 20 copies · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.69 | 0.83 | 55 | SX0, UNX |
| 2 | 97 | 0.43 | 0.78 | 16 | empty |
| 3 | 51 | 0.33 | 0.78 | 13 | UNX |
Compared structures
- 3SX0 · Crystal structure of Dot1l in complex with a brominated SAH analog · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TEK3 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase, H3 lysine-79… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8TEK3
- Elsewhere: RCSB PDB 3SX0 · PDBe 3SX0 · UniProt Q8TEK3
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