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Linked KDM5A jmj domain bound to the inhibitor N44 I.E. 3-((2- (pyridin-2-yl)-6-(4-(vinylsulfonyl)-1,4-diazepan-1-YL)PYRIMIDIN-4- YL)AMINO)PROPANOIC acid
Analyse Linked KDM5A jmj domain bound to the inhibitor N44 I.E. 3-((2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DQ6
- Type
- protein
- Length
- 298 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Linked KDM5A jmj domain
- EC
- 1.14.11.-
- UniProt
- P29375
- Ligands
- H6J, 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 | Linked KDM5A jmj domain (EC 1.14.11.-) | protein | 298 | 32% helix, 23% strand | P29375 |
Ligands and binding sites
- H6J · N-{6-[4-(ethenylsulfonyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine · 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 | 400 | 0.67 | 0.80 | 47 | H6J, MN |
| 2 | 83 | 0.42 | 0.79 | 20 | empty |
| 3 | 63 | 0.37 | 0.79 | 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 6DQ6 · PDBe 6DQ6 · UniProt P29375
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