MolNFT v1 · #119534 · protein
Crystal structure of the catalytic domain of human JARID1B in complex with maybridge fragment 2,4-dichloro-N-pyridin-3-ylbenzamide (E48115B) (ligand modelled based on pandda event MAP)
5FZ1 · Lysine-specific demethylase 5B, lysine-specific demethylase…: “Crystal structure of the catalytic domain of human JARID1B in complex with maybridge fragment…”. X-ray diffraction, 4 ligands (W77, ZN, MN), 5 pockets (best druggability…
- PDB
- 5FZ1
- Type
- protein
- Length
- 454 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5B, lysine-specific demethylase 5B
- EC
- 1.14.11.-
- UniProt
- Q9UGL1
- Ligands
- W77, ZN, MN, PO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B, lysine-specific demethylase 5B (EC 1.14.11.-) | protein | 454 | 37% helix, 20% strand | Q9UGL1 |
Ligands and binding sites
- W77 · 2,4-dichloro-N-(pyridin-3-yl)benzamide · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 12 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.79 | 0.87 | 47 | DMS, EDO, W77 |
| 2 | 351 | 0.77 | 0.87 | 31 | DMS, EDO |
| 3 | 199 | 0.75 | 0.90 | 23 | EDO |
| 4 | 137 | 0.44 | 0.76 | 23 | empty |
| 5 | 86 | 0.36 | 0.75 | 20 | EDO |
Compared structures
- 5FZ1 · Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UGL1 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5B (Q9UGL1) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9UGL1
- Elsewhere: RCSB PDB 5FZ1 · PDBe 5FZ1 · UniProt Q9UGL1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.