MolNFT v1 · #150814 · protein
Crystal structure of human KDM5B in complex with compound 16A
6H4Z · Lysine-specific demethylase 5B,LYSINE-specific demethylase…: “Crystal structure of human KDM5B in complex with compound 16A”. X-ray diffraction, 3 ligands (FQ5, MN, ZN), 6 pockets (best druggability 0.82). MolNFT v1 #150814 on…
- PDB
- 6H4Z
- Type
- protein
- Length
- 458 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
- FQ5, MN, ZN
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 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 | 458 | 38% helix, 20% strand | Q9UGL1 |
Ligands and binding sites
- FQ5 · 8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one · ligand · 2 copies · chains A
- MN · Manganese (II) ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 9 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.82 | 0.84 | 62 | MN, FQ5, DMS, EDO |
| 2 | 220 | 0.76 | 0.90 | 24 | EDO, MN |
| 3 | 73 | 0.42 | 0.80 | 22 | DMS |
| 4 | 111 | 0.37 | 0.74 | 20 | empty |
| 5 | 62 | 0.36 | 0.78 | 14 | empty |
Compared structures
- 6H4Z · Crystal structure of human KDM5B in complex with compound 16a · 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 Q9UGL1
- Elsewhere: RCSB PDB 6H4Z · PDBe 6H4Z · UniProt Q9UGL1
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