MolNFT v1 · #146727 · protein
Linked KDM5A jmj domain bound to the inhibitor gsk-J1
6DQ4: “Linked KDM5A jmj domain bound to the inhibitor gsk-J1”. X-ray diffraction, 3 ligands (K0I, MN, SO4), 3 pockets (best druggability 0.64). MolNFT v1 #146727 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DQ4
- Type
- protein
- Length
- 312 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
- K0I, MN, SO4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Linked KDM5A jmj domain (EC 1.14.11.-) | protein | 312 | 32% helix, 22% strand | P29375 |
Ligands and binding sites
- K0I · 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A
- DMS · Dimethyl sulfoxide · 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 | 364 | 0.64 | 0.79 | 39 | K0I, MN, GOL, DMS |
| 2 | 115 | 0.49 | 0.80 | 21 | empty |
| 3 | 56 | 0.38 | 0.81 | 20 | 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 6DQ4 · PDBe 6DQ4 · UniProt P29375
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