Research workbench
Crystal structure of KDM4D with tetrazolhydrazide compound 6
Analyse Crystal structure of KDM4D with tetrazolhydrazide compound 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ETG
- Type
- protein
- Length
- 331 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.279
- Source
- Homo sapiens
- Molecule
- Lysine-specific demethylase 4D
- EC
- 1.14.11.-
- UniProt
- Q6B0I6
- Ligands
- BWT, ZN, NI, NA, SO4, CL
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.279 · 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 | 331 | 31% helix, 26% strand | Q6B0I6 |
Ligands and binding sites
- BWT · [[4-(2~{H}-1,2,3,4-tetrazol-5-yl) phenyl]carbonylamino]azanium · ligand · chains A
- ZN · Zinc ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 9 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 | 527 | 0.77 | 0.84 | 55 | NI, EDO, BWT |
| 2 | 53 | 0.48 | 0.86 | 18 | empty |
| 3 | 71 | 0.38 | 0.78 | 19 | EDO |
Compared structures
- 6ETG · Crystal structure of KDM4D with tetrazolhydrazide compound 6 · 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 6ETG · PDBe 6ETG · UniProt Q6B0I6
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