MolNFT v1 · #119389 · protein
Crystal structure of human JARID1B in complex with GSK467
5FUN · Lysine-specific demethylase 5B: “Crystal structure of human JARID1B in complex with GSK467”. X-ray diffraction, 5 ligands (GZA, ZN, MN), 5 pockets (best druggability 0.81). MolNFT v1 #119389 on GenesisL1: 3D structure, binding sites…
- PDB
- 5FUN
- Type
- protein
- Length
- 455 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5B
- EC
- 1.14.11.-
- UniProt
- Q9UGL1
- Ligands
- GZA, ZN, MN, NA, PO4
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B (EC 1.14.11.-) | protein | 455 | 35% helix, 19% strand | Q9UGL1 |
Ligands and binding sites
- GZA · 2-[(1-benzyl-1H-pyrazol-4-yl)oxy]pyrido[3,4-d]pyrimidin-4(3H)-one · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.81 | 0.84 | 70 | GZA, MN, EPE |
| 2 | 184 | 0.74 | 0.90 | 22 | empty |
| 3 | 63 | 0.41 | 0.81 | 21 | EDO |
| 4 | 81 | 0.36 | 0.76 | 19 | empty |
| 5 | 59 | 0.34 | 0.77 | 17 | 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 Q9UGL1
- Elsewhere: RCSB PDB 5FUN · PDBe 5FUN · UniProt Q9UGL1
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