MolNFT v1 · #122660 · protein
Linked KDM5A jmj domain bound to the inhibitor N19 [2-(5-((4-chloro-2- METHYLBENZYL)OXY)-1H-pyrazol-1-YL)ISONICOTINIC acid]
5IW0 · Lysine-specific demethylase 5A: “Linked KDM5A jmj domain bound to the inhibitor N19 [2-(5-((4-chloro-2…”. X-ray diffraction, 3 ligands (6EP, AKG, MN), 3 pockets (best druggability 0.67). MolNFT v1 #122660 on GenesisL1: 3D structure…
- PDB
- 5IW0
- Type
- protein
- Length
- 306 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5A
- EC
- 1.14.11.-
- UniProt
- P29375
- Ligands
- 6EP, AKG, MN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5A (EC 1.14.11.-) | protein | 306 | 32% helix, 23% strand | P29375 |
Ligands and binding sites
- 6EP · 2-{5-[(4-chloro-2-methylphenyl)methoxy]-1H-pyrazol-1-yl}pyridine-4-carboxylic acid · ligand · chains A
- AKG · 2-oxoglutaric acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.67 | 0.79 | 50 | 6EP, AKG, MN, GOL |
| 2 | 51 | 0.38 | 0.81 | 17 | empty |
| 3 | 83 | 0.38 | 0.77 | 19 | EDO |
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 P29375
- Elsewhere: RCSB PDB 5IW0 · PDBe 5IW0 · UniProt P29375
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