MolNFT v1 · #150674 · protein
Crystal structure of KDM4D with tetrazolylhydrazide ligand AA040
6H0X · Lysine-specific demethylase 4D: “Crystal structure of KDM4D with tetrazolylhydrazide ligand AA040”. X-ray diffraction, 4 ligands (FJB, ZN, NI), 3 pockets (best druggability 0.76). MolNFT v1 #150674 on GenesisL1: 3D structure…
- PDB
- 6H0X
- Type
- protein
- Length
- 329 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4D
- EC
- 1.14.11.-
- UniProt
- Q6B0I6
- Ligands
- FJB, ZN, NI, CL
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4D (EC 1.14.11.-) | protein | 329 | 32% helix, 25% strand | Q6B0I6 |
Ligands and binding sites
- FJB · [[(2~{R})-2-(5-phenylpentanoylamino)-2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoyl]amino]azanium · ligand · chains A
- ZN · Zinc ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 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 | 199 | 0.76 | 0.91 | 37 | EDO, NI, FJB |
| 2 | 74 | 0.47 | 0.82 | 25 | empty |
| 3 | 68 | 0.33 | 0.76 | 23 | empty |
Compared structures
- 6H0X · Crystal Structure of KDM4D with tetrazolylhydrazide ligand AA040 · the same entry in another collection · chain A against A, TM-score 1.00
- Q6B0I6 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 4D (Q6B0I6) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 6H0X · PDBe 6H0X · UniProt Q6B0I6
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