Research workbench
Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone lysine demethylases
Analyse Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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