MolNFT v1 · #147629 · protein
Crystal structure of KDM5B in complex with KDOPZ000049A.
6EJ0 · Lysine-specific demethylase 5B,LYSINE-specific demethylase…: “Crystal structure of KDM5B in complex with KDOPZ000049A.”. X-ray diffraction, 3 ligands (B7K, MN, ZN), 5 pockets (best druggability 0.80). MolNFT v1 #147629 on GenesisL1…
- PDB
- 6EJ0
- Type
- protein
- Length
- 453 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5B,LYSINE-specific demethylase 5B
- EC
- 1.14.11.-
- UniProt
- Q9UGL1
- Ligands
- B7K, MN, ZN
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 37% 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 | 453 | 37% helix, 20% strand | Q9UGL1 |
Ligands and binding sites
- B7K · 7-oxidanylidene-6-propan-2-yl-5-[1-(1-prop-2-enoylpiperidin-4-yl)pyrazol-4-yl]-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.80 | 0.83 | 67 | DMS, B7K |
| 2 | 179 | 0.73 | 0.90 | 24 | EDO |
| 3 | 129 | 0.45 | 0.77 | 22 | empty |
| 4 | 53 | 0.41 | 0.82 | 19 | DMS |
| 5 | 53 | 0.31 | 0.76 | 14 | EDO |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 6EJ0 · PDBe 6EJ0 · UniProt Q9UGL1
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