Research workbench
Crystal structure of LSD1 in complex with trans-2- pentafluorophenylcyclopropylamine
Analyse Crystal structure of LSD1 in complex with trans-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ABT
- Type
- protein
- Length
- 643 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1
- UniProt
- O60341
- Ligands
- 2PF
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1 | protein | 643 | 43% helix, 16% strand | O60341 |
Ligands and binding sites
- 2PF · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-(pentafluorophenyl)-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate · ligand · 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 | 1046 | 0.82 | 0.83 | 89 | 2PF |
| 2 | 331 | 0.62 | 0.78 | 29 | empty |
| 3 | 132 | 0.39 | 0.74 | 19 | empty |
| 4 | 78 | 0.38 | 0.77 | 16 | empty |
| 5 | 55 | 0.26 | 0.73 | 13 | empty |
Compared structures
- 3ABT · Crystal Structure of LSD1 in complex with trans-2-pentafluorophenylcyclopropylamine · 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 3ABT · PDBe 3ABT · UniProt O60341
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.