MolNFT v1 · #119208 · protein
Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone lysine demethylases
5FP3 · Human lysine-specific demethylase 6B, JMJD3: “Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone lysine demethylases”. X-ray diffraction, 5 ligands (BCN, YC8, MG), 9 pockets (best druggability 0.72).…
- PDB
- 5FP3
- Type
- protein
- Length
- 858 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human lysine-specific demethylase 6B, JMJD3
- EC
- 1.14.11.-
- UniProt
- O15054
- Ligands
- BCN, YC8, MG, ZN, CO
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human lysine-specific demethylase 6B, JMJD3 (EC 1.14.11.-) | protein | 435 | 34% helix, 24% strand | O15054 |
| B | Human lysine-specific demethylase 6B, JMJD3 (EC 1.14.11.-) | protein | 423 | 35% helix, 24% strand | O15054 |
Ligands and binding sites
- BCN · Bicine · ligand · 4 copies · chains A, B
- YC8 · 3-(4-phenylbutanoylamino)pyridine-4-carboxylic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.72 | 0.81 | 48 | YC8, BCN, MG, CO |
| 2 | 528 | 0.70 | 0.79 | 46 | YC8, BCN, MG, CO |
| 3 | 357 | 0.59 | 0.76 | 50 | empty |
| 4 | 185 | 0.51 | 0.77 | 24 | empty |
| 5 | 66 | 0.38 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 288 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FP3 · Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone… · the same entry in another collection · chain A against A, TM-score 1.00
- O15054 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 6B (O15054) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O15054
- Elsewhere: RCSB PDB 5FP3 · PDBe 5FP3 · UniProt O15054
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