Research workbench
Crystal structure of human KDM5B in complex with compound 34a
Analyse Crystal structure of human KDM5B in complex with compound 34a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H50
- Type
- protein
- Length
- 456 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.19
- Source
- Homo sapiens
- Molecule
- Lysine-specific demethylase 5B,Lysine-specific demethylase 5B
- EC
- 1.14.11.-
- UniProt
- Q9UGL1
- Ligands
- FO2, ZN, MN, PO4
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.19 · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B,Lysine-specific demethylase 5B (EC 1.14.11.-) | protein | 456 | 38% helix, 20% strand | Q9UGL1 |
Ligands and binding sites
- FO2 · 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 5 copies · 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.83 | 0.85 | 66 | MN, FO2, DMS |
| 2 | 186 | 0.74 | 0.90 | 23 | empty |
| 3 | 100 | 0.40 | 0.76 | 26 | empty |
| 4 | 59 | 0.34 | 0.77 | 17 | empty |
Compared structures
- 6H50 · Crystal structure of human KDM5B in complex with compound 34A · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UGL1 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5B (Q9UGL1) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9UGL1
- Elsewhere: RCSB PDB 6H50 · PDBe 6H50 · UniProt Q9UGL1
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