MolNFT v1 · #88821 · protein
Crystal structure of human JMJD2D in complex with N-oxalylglycine and bound O-toluenesulfonamide
4D6R · Lysine-specific demethylase 4D: “Crystal structure of human JMJD2D in complex with N-oxalylglycine and bound O-toluenesulfonamide”. X-ray diffraction, 4 ligands (IEJ, OGA, ZN), 3 pockets (best druggability 0.75). MolNFT v1 #88821 on…
- PDB
- 4D6R
- Type
- protein
- Length
- 323 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4D
- UniProt
- Q6B0I6
- Ligands
- IEJ, OGA, ZN, NI
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4D | protein | 323 | 30% helix, 25% strand | Q6B0I6 |
Ligands and binding sites
- IEJ · O-toluenesulfonamide · ligand · 3 copies · chains A
- OGA · N-oxalylglycine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.75 | 0.84 | 55 | NI, EDO, OGA |
| 2 | 58 | 0.49 | 0.85 | 20 | empty |
| 3 | 82 | 0.37 | 0.77 | 25 | EDO |
Compared structures
- 4D6R · crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6B0I6
- Elsewhere: RCSB PDB 4D6R · PDBe 4D6R · UniProt Q6B0I6
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