Research workbench
MLL1 set N3861I/Q3867L bound to inhibitor 18 (tc-5153)
Analyse MLL1 set N3861I/Q3867L bound to inhibitor 18 (tc-5153) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U9K
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase
- EC
- 2.1.1.43
- UniProt
- B4DIJ7
- Ligands
- Q2V, ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase (EC 2.1.1.43) | protein | 149 | 19% helix, 35% strand | B4DIJ7 |
| B | Histone-lysine N-methyltransferase (EC 2.1.1.43) | protein | 149 | 20% helix, 35% strand | B4DIJ7 |
Ligands and binding sites
- Q2V · 5'-([(3S)-3-amino-3-carboxypropyl]{[1-(3,3-diphenylpropyl)azetidin-3-yl]methyl}amino)-5'-deoxyadenosine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.69 | 0.86 | 34 | GOL |
| 2 | 326 | 0.58 | 0.76 | 40 | Q2V |
| 3 | 225 | 0.48 | 0.74 | 28 | Q2V |
Interfaces
1 interface between chains.
- A–B · 587 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6U9K · MLL1 SET N3861I/Q3867L bound to inhibitor 18 (TC-5153) · 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
- Every structure of UniProt B4DIJ7
- Elsewhere: RCSB PDB 6U9K · PDBe 6U9K · UniProt B4DIJ7
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