MolNFT v1 · #107593 · protein
Crystal structure of jmjc domain of human histone demethylase uty in complex with epitherapuetic compound 2-(((2-((2-(DIMETHYLAMINO)ETHYL) (ETHYL)AMINO)-2-OXOETHYL)AMINO)METHYL)ISONICOTINIC acid.
4UF0: “Crystal structure of jmjc domain of human histone demethylase uty in complex with epitherapuetic compound…”. X-ray diffraction, 3 ligands (MMK, FE2, ZN), 9 pockets (best druggability 0.80). MolNFT v1 #107593 on GenesisL1: 3D…
- PDB
- 4UF0
- Type
- protein
- Length
- 880 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone demethylase uty
- EC
- 1.14.11.-
- UniProt
- O14607
- Ligands
- MMK, FE2, ZN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone demethylase uty (EC 1.14.11.-) | protein | 442 | 37% helix, 24% strand | O14607 |
| B | Histone demethylase uty (EC 1.14.11.-) | protein | 438 | 36% helix, 24% strand | O14607 |
Ligands and binding sites
- MMK · 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 20 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 | 1139 | 0.80 | 0.81 | 115 | EDO |
| 2 | 580 | 0.73 | 0.81 | 60 | FE2, MMK |
| 3 | 578 | 0.73 | 0.81 | 58 | FE2, MMK, EDO |
| 4 | 237 | 0.58 | 0.79 | 25 | empty |
| 5 | 97 | 0.45 | 0.79 | 22 | EDO |
Interfaces
1 interface between chains.
- A–B · 1053 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4UF0 · Crystal structure of JmjC domain of human histone demethylase UTY in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O14607 · AlphaFold monomer V2.0 prediction for histone demethylase uty (O14607) · 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 O14607
- Elsewhere: RCSB PDB 4UF0 · PDBe 4UF0 · UniProt O14607
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