MolNFT v1 · #119018 · protein
Crystal structure of human JMJD2C catalytic domain in complex with epitherapuetic compound 2-(((2-((2-( DIMETHYLAMINO)ETHYL) (ETHYL)AMINO)-2-OXOETHYL)AMINO)METHYL) isonicotinic acid
5FJH · Lysine-specific demethylase 4C: “Crystal structure of human JMJD2C catalytic domain in complex with epitherapuetic compound 2-(((2-((2-(…”. X-ray diffraction, 4 ligands (MMK, NI, ZN), 4 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 5FJH
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4C
- EC
- 1.14.11.-
- UniProt
- Q9H3R0
- Ligands
- MMK, NI, ZN, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine-specific demethylase 4C (EC 1.14.11.-) | protein | 338 | 31% helix, 25% strand | Q9H3R0 |
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
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.70 | 0.82 | 39 | NI, MMK |
| 2 | 380 | 0.70 | 0.82 | 39 | NI, MMK |
| 3 | 87 | 0.54 | 0.85 | 20 | empty |
| 4 | 76 | 0.49 | 0.83 | 23 | empty |
Compared structures
- 5FJH · Crystal structure of human JMJD2C catalytic domain in complex with epitherapuetic… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H3R0 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 4C (Q9H3R0) · a predicted model of the same protein · chain A 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 Q9H3R0
- Elsewhere: RCSB PDB 5FJH · PDBe 5FJH · UniProt Q9H3R0
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