Research workbench
Crystal structure of KDM4D with tetrazolylhydrazide ligand NR073
Analyse Crystal structure of KDM4D with tetrazolylhydrazide ligand NR073 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H10
- Type
- protein
- Length
- 330 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
- FJ8, ZN, NA, NI, CL, SO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4D (EC 1.14.11.-) | protein | 330 | 31% helix, 26% strand | Q6B0I6 |
Ligands and binding sites
- FJ8 · ~{N}-[(~{E})-(4-methylphenyl)methylideneamino]-2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanamide · ligand · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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 | 489 | 0.75 | 0.83 | 51 | EDO, NI, FJ8 |
| 2 | 52 | 0.48 | 0.86 | 15 | empty |
| 3 | 70 | 0.35 | 0.76 | 24 | EDO |
Compared structures
- 6H10 · Crystal Structure of KDM4D with tetrazolylhydrazide ligand NR073 · 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 6H10 · PDBe 6H10 · UniProt Q6B0I6
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