MolNFT v1 · #144020 · protein
Linked KDM5A jmj domain bound to the inhibitor 2-((2-CHLOROPHENYL)(2- (piperidin-1-YL)ETHOXY)METHYL)-1L2-PYRROLO[3,2-B]PYRIDINE-7- carboxylic acid (compound N40)
6BGV · Lysine-specific demethylase 5A, linked KDM5A jmj domain: “Linked KDM5A jmj domain bound to the inhibitor 2-((2-CHLOROPHENYL)(2…”. X-ray diffraction, 2 ligands (DQG, MN), 4 pockets (best druggability 0.67). MolNFT v1 #144020 on…
- PDB
- 6BGV
- Type
- protein
- Length
- 309 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
- DQG, MN
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5A, linked KDM5A jmj domain (EC 1.14.11.-) | protein | 309 | 30% helix, 23% strand | P29375 |
Ligands and binding sites
- DQG · 2-{(S)-(2-chlorophenyl)[2-(piperidin-1-yl) ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.67 | 0.80 | 49 | DQG, MN, EDO |
| 2 | 88 | 0.41 | 0.77 | 14 | GOL |
| 3 | 58 | 0.40 | 0.81 | 16 | GOL |
| 4 | 61 | 0.38 | 0.80 | 19 | 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 6BGV · PDBe 6BGV · UniProt P29375
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