MolNFT v1 · #125700 · protein
THIENO[3,2-B]PYRROLE-5-carboxamides as novel reversible inhibitors of histone lysine demethylase KDM1A/LSD1: compound 34
5LGU · Lysine-specific histone demethylase 1A: “THIENO[3,2-B]PYRROLE-5-carboxamides as novel reversible inhibitors of histone lysine demethylase KDM1A/LSD1…”. X-ray diffraction, 2 ligands (FAD, 6W1), 9 pockets (best druggability 0.81).…
- PDB
- 5LGU
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A; Rest corepressor 1
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- FAD, 6W1
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 666 | 44% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 62% helix, 0% strand | Q9UKL0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- 6W1 · 4-methyl-~{N}-[2-[[4-[[(3~{R})-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.81 | 0.82 | 91 | FAD, 6W1 |
| 2 | 367 | 0.61 | 0.77 | 33 | empty |
| 3 | 228 | 0.50 | 0.75 | 28 | empty |
| 4 | 85 | 0.47 | 0.81 | 21 | empty |
| 5 | 109 | 0.44 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2745 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5LGU · Thieno[3,2-b]pyrrole-5-carboxamides as Novel Reversible Inhibitors of Histone Lysine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKL0 · AlphaFold monomer V2.0 prediction for rest corepressor 1 (Q9UKL0) · a predicted model of the same protein · chain B against A, TM-score 0.95
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
- Every structure of UniProt Q9UKL0
- Elsewhere: RCSB PDB 5LGU · PDBe 5LGU · UniProt O60341 · UniProt Q9UKL0
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