MolNFT v1 · #158349 · protein
Human LSD1 in complex with phenelzine sulfate
6NR5 · Lysine-specific histone demethylase 1A: “Human LSD1 in complex with phenelzine sulfate”. X-ray diffraction, 1 ligand (KXM), 5 pockets (best druggability 0.82). MolNFT v1 #158349 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6NR5
- Type
- protein
- Length
- 636 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A
- EC
- 1.-.-.-
- UniProt
- O60341
- Ligands
- KXM
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 636 | 46% helix, 17% strand | O60341 |
Ligands and binding sites
- KXM · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R)-5-[(4AR)-7,8-dimethyl-2,4-dioxo-5-(2-phenylethyl)-3,4, 4A,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) · 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 | 923 | 0.82 | 0.84 | 93 | KXM |
| 2 | 302 | 0.61 | 0.79 | 21 | empty |
| 3 | 88 | 0.42 | 0.78 | 17 | empty |
| 4 | 61 | 0.37 | 0.79 | 19 | empty |
| 5 | 93 | 0.33 | 0.73 | 19 | empty |
Compared structures
- 6NR5 · Human LSD1 in complex with Phenelzine sulfate · 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 6NR5 · PDBe 6NR5 · UniProt O60341
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