MolNFT v1 · #144030 · protein
Linked KDM5A jmj domain bound to the inhibitor 2-((2-CHLOROPHENYL)(3- (piperidin-1-YL)PROPOXY)METHYL)-1H-PYRROLO[3,2-B]PYRIDINE-7- carboxylic acid (compound N48)
6BH5 · Lysine-specific demethylase 5A, linked KDM5A jmj domain: “Linked KDM5A jmj domain bound to the inhibitor 2-((2-CHLOROPHENYL)(3…”. X-ray diffraction, 2 ligands (DNY, MN), 2 pockets (best druggability 0.66). MolNFT v1 #144030 on…
- PDB
- 6BH5
- Type
- protein
- Length
- 292 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5A, linked KDM5A jmj domain
- EC
- 1.14.11.-
- UniProt
- P29375
- Ligands
- DNY, MN
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5A, linked KDM5A jmj domain (EC 1.14.11.-) | protein | 292 | 32% helix, 24% strand | P29375 |
Ligands and binding sites
- DNY · 2-{(S)-(2-chlorophenyl)[3-(piperidin-1-yl) propoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.66 | 0.80 | 48 | DNY, MN, GOL |
| 2 | 108 | 0.41 | 0.76 | 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 6BH5 · PDBe 6BH5 · UniProt P29375
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