MolNFT v1 · #165893 · protein
MLL1 set N3861I/Q3867L bound to inhibitor 16 (tc-5109)
6U9M · Histone-lysine N-methyltransferase: “MLL1 set N3861I/Q3867L bound to inhibitor 16 (tc-5109)”. X-ray diffraction, 2 ligands (Q2M, ZN), 3 pockets (best druggability 0.69). MolNFT v1 #165893 on GenesisL1: 3D structure, binding sites…
- PDB
- 6U9M
- Type
- protein
- Length
- 297 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
- Q2M, ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase (EC 2.1.1.43) | protein | 148 | 20% helix, 34% strand | B4DIJ7 |
| B | Histone-lysine N-methyltransferase (EC 2.1.1.43) | protein | 149 | 17% helix, 35% strand | B4DIJ7 |
Ligands and binding sites
- Q2M · 5'-{[(3S)-3-amino-3-carboxypropyl]({1-[(thiophen-2-yl) methyl]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 | 251 | 0.69 | 0.85 | 37 | GOL |
| 2 | 327 | 0.58 | 0.77 | 37 | Q2M |
| 3 | 221 | 0.48 | 0.74 | 29 | Q2M |
Interfaces
1 interface between chains.
- A–B · 547 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6U9M · MLL1 SET N3861I/Q3867L bound to inhibitor 16 (TC-5109) · 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 6U9M · PDBe 6U9M · UniProt B4DIJ7
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