Research workbench
LSD1-tranylcypromine complex
Analyse LSD1-tranylcypromine complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EJR
- 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
- EC
- 1.-.-.-
- UniProt
- O60341
- Ligands
- F2N
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1 (EC 1.-.-.-) | protein | 643 | 43% helix, 17% strand | O60341 |
Ligands and binding sites
- F2N · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[7,8-dimethyl-2,4-dioxo-5-(3-phenylpropanoyl)-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl 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 | 991 | 0.82 | 0.83 | 88 | F2N |
| 2 | 345 | 0.62 | 0.78 | 27 | empty |
| 3 | 113 | 0.49 | 0.80 | 21 | empty |
| 4 | 101 | 0.36 | 0.74 | 22 | empty |
| 5 | 59 | 0.27 | 0.73 | 12 | empty |
Compared structures
- 2EJR · LSD1-tranylcypromine complex · 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 2EJR · PDBe 2EJR · UniProt O60341
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