MolNFT v1 · #119233 · protein
Crystal structure of human JARID1B in complex with GSKJ1
5FPU · Lysine-specific demethylase 5B: “Crystal structure of human JARID1B in complex with GSKJ1”. X-ray diffraction, 4 ligands (K0I, ZN, MN), 5 pockets (best druggability 0.77). MolNFT v1 #119233 on GenesisL1: 3D structure, binding sites…
- PDB
- 5FPU
- Type
- protein
- Length
- 455 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5B
- UniProt
- Q9UGL1
- Ligands
- K0I, ZN, MN, PO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B | protein | 455 | 37% helix, 20% strand | Q9UGL1 |
Ligands and binding sites
- K0I · 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.77 | 0.84 | 52 | K0I, MN, PO4 |
| 2 | 153 | 0.73 | 0.91 | 23 | EDO |
| 3 | 251 | 0.73 | 0.87 | 32 | EPE |
| 4 | 192 | 0.56 | 0.80 | 33 | empty |
| 5 | 67 | 0.32 | 0.75 | 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 5FPU · PDBe 5FPU · UniProt Q9UGL1
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