MolNFT v1 · #108057 · protein
LSD1(KDM1A)-corest in complex with 1-methyl-tranylcypromine (1S,2R)
4UVB · Lysine-specific histone demethylase 1A: “LSD1(KDM1A)-corest in complex with 1-methyl-tranylcypromine (1S,2R)”. X-ray diffraction, 1 ligand (D51), 8 pockets (best druggability 0.83). MolNFT v1 #108057 on GenesisL1: 3D structure…
- PDB
- 4UVB
- 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
- D51
- Pockets
- 8 · best druggability 0.83
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
- D51 · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,7aS)-1-amino-1,10,11-trimethyl-4,6-dioxo-3-phenyl-2,3,5,6,7,7a-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.83 | 0.83 | 92 | D51 |
| 2 | 333 | 0.61 | 0.78 | 29 | empty |
| 3 | 189 | 0.47 | 0.75 | 24 | empty |
| 4 | 90 | 0.46 | 0.80 | 16 | empty |
| 5 | 82 | 0.39 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2783 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
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 4UVB · PDBe 4UVB · UniProt O60341 · UniProt Q9UKL0
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