MolNFT v1 · #146738 · protein
Linked KDM5A jmj domain bound to the inhibitor N68 I.E. 2-(1-(2- (piperidin-1-YL)ETHYL)-1H-BENZO[D]IMIDAZOL-2-YL)THIENO[3,2- B]PYRIDINE-7-carboxylic acid
6DQF: “Linked KDM5A jmj domain bound to the inhibitor N68 I.E. 2-(1-(2…”. X-ray diffraction, 2 ligands (H61, MN), 3 pockets (best druggability 0.65). MolNFT v1 #146738 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DQF
- Type
- protein
- Length
- 294 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
- H61, MN
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Linked KDM5A jmj domain (EC 1.14.11.-) | protein | 294 | 30% helix, 24% strand | P29375 |
Ligands and binding sites
- H61 · 2-{1-[2-(piperidin-1-yl)ethyl]-1H-benzimidazol-2-yl}thieno[3,2-b]pyridine-7-carboxylic acid · 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 | 340 | 0.65 | 0.80 | 42 | H61, MN |
| 2 | 94 | 0.44 | 0.79 | 18 | empty |
| 3 | 54 | 0.31 | 0.77 | 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 6DQF · PDBe 6DQF · UniProt P29375
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