MolNFT v1 · #119214 · protein
Crystal structure of human KDM4D in complex with 3- aminopyridine-4-carboxylic acid
5FP9 · Human lysine-specific demethylase 4D jmjc domain-containing…: “Crystal structure of human KDM4D in complex with 3- aminopyridine-4-carboxylic acid”. X-ray diffraction, 4 ligands (4SV, ZN, CO), 2 pockets (best druggability 0.73).…
- PDB
- 5FP9
- Type
- protein
- Length
- 327 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human lysine-specific demethylase 4D jmjc domain-containing histone demethylation protein…
- EC
- 1.14.11.-
- UniProt
- Q6B0I6
- Ligands
- 4SV, ZN, CO, SO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human lysine-specific demethylase 4D jmjc domain-containing histone demethylation protein 3D, jumonji domain-containing protein 2D, JMJD2D (EC 1.14.11.-) | protein | 327 | 32% helix, 25% strand | Q6B0I6 |
Ligands and binding sites
- 4SV · 3-aminopyridine-4-carboxylic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CO · Cobalt (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.73 | 0.82 | 50 | CO, 4SV, SO4 |
| 2 | 87 | 0.34 | 0.74 | 26 | GOL |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5FP9 · Crystal structure of human KDM4D in complex with 3-aminopyridine-4- carboxylic acid · 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 5FP9 · PDBe 5FP9 · UniProt Q6B0I6
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