MolNFT v1 · #122644 · protein
Linked KDM5A jmj domain bound to the inhibitor N11 [3-({1-[2-(4,4- difluoropiperidin-1-YL)ETHYL]-5-fluoro-1H-indazol-3-YL}AMINO) pyridine-4-carboxylic acid]
5IVJ · Lysine-specific demethylase 5A: “Linked KDM5A jmj domain bound to the inhibitor N11 [3-({1-[2-(4,4…”. X-ray diffraction, 2 ligands (6ED, MN), 3 pockets (best druggability 0.65). MolNFT v1 #122644 on GenesisL1: 3D structure, binding…
- PDB
- 5IVJ
- Type
- protein
- Length
- 296 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
- 6ED, MN
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5A (EC 1.14.11.-) | protein | 296 | 31% helix, 24% strand | P29375 |
Ligands and binding sites
- 6ED · 3-({1-[2-(4,4-difluoropiperidin-1-yl)ethyl]-5-fluoro-1H-indazol-3-yl}amino)pyridine-4-carboxylic acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · chains A
- DMS · Dimethyl sulfoxide · additive · 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 | 352 | 0.65 | 0.80 | 47 | 6ED |
| 2 | 91 | 0.38 | 0.76 | 16 | empty |
| 3 | 57 | 0.38 | 0.80 | 21 | empty |
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 5IVJ · PDBe 5IVJ · UniProt P29375
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