Research workbench
Linked KDM5A jmj domain bound to the inhibitor N10 8-(1-methyl-1H- imidazol-4-yl)-2-(4,4,4-TRIFLUOROBUTOXY)PYRIDO[3,4-D]PYRIMIDIN-4-ol
Analyse Linked KDM5A jmj domain bound to the inhibitor N10 8-(1-methyl-1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IVF
- Type
- protein
- Length
- 308 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
- 6EB, MN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5A (EC 1.14.11.-) | protein | 308 | 31% helix, 23% strand | P29375 |
Ligands and binding sites
- 6EB · 8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4-ol · ligand · chains A
- MN · Manganese (II) ion · metal · 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 | 387 | 0.68 | 0.81 | 48 | 6EB, MN |
| 2 | 52 | 0.37 | 0.80 | 19 | empty |
| 3 | 77 | 0.36 | 0.76 | 17 | 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 5IVF · PDBe 5IVF · UniProt P29375
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