MolNFT v1 · #147616 · protein
Crystal structure of KDM5B in complex with S49365A.
6EIN · Lysine-specific demethylase 5B,LYSINE-specific demethylase…: “Crystal structure of KDM5B in complex with S49365A.”. X-ray diffraction, 3 ligands (B7Z, MN, ZN), 5 pockets (best druggability 0.75). MolNFT v1 #147616 on GenesisL1: 3D…
- PDB
- 6EIN
- Type
- protein
- Length
- 439 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
- B7Z, MN, ZN
- Pockets
- 5 · best druggability 0.75
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 | 439 | 37% helix, 20% strand | Q9UGL1 |
Ligands and binding sites
- B7Z · 8-[4-[2-(4-propanoylpiperazin-1-yl)ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 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 | 208 | 0.75 | 0.90 | 23 | EDO |
| 2 | 307 | 0.61 | 0.79 | 34 | B7Z, MN |
| 3 | 90 | 0.45 | 0.80 | 21 | empty |
| 4 | 163 | 0.45 | 0.75 | 22 | EDO |
| 5 | 64 | 0.33 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
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 6EIN · PDBe 6EIN · UniProt Q9UGL1
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