MolNFT v1 · #189687 · protein
Crystal structure of LSD1 in complex with compound 5
7VQT · Lysine-specific histone demethylase 1A: “Crystal structure of LSD1 in complex with compound 5”. X-ray diffraction, 2 ligands (7UW, FAD), 5 pockets (best druggability 0.81). MolNFT v1 #189687 on GenesisL1: 3D structure, binding sites…
- PDB
- 7VQT
- Type
- protein
- Length
- 647 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A
- EC
- 1.14.99.66
- UniProt
- O60341
- Ligands
- 7UW, FAD
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.14.99.66) | protein | 647 | 46% helix, 18% strand | O60341 |
Ligands and binding sites
- 7UW · 3-[3,5-bis(fluoranyl)-2-[(2-fluoranylpyridin-4-yl) methoxy]phenyl]propanal · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- TLA · L(+)-tartaric acid · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.81 | 0.82 | 88 | GOL, 7UW, FAD |
| 2 | 339 | 0.61 | 0.78 | 27 | empty |
| 3 | 89 | 0.42 | 0.78 | 16 | empty |
| 4 | 103 | 0.39 | 0.76 | 19 | TLA |
| 5 | 64 | 0.35 | 0.77 | 13 | GOL |
Compared structures
- 7VQT · Crystal structure of LSD1 in complex with compound 5 · 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 O60341
- Elsewhere: RCSB PDB 7VQT · PDBe 7VQT · UniProt O60341
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