Research workbench
Crystal structure of KDM4B in complex with QC6352
Analyse Crystal structure of KDM4B in complex with QC6352 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JM5
- Type
- protein
- Length
- 682 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4B
- EC
- 1.14.11.66
- UniProt
- O94953
- Ligands
- 9DJ, NI, ZN
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4B (EC 1.14.11.66) | protein | 343 | 30% helix, 24% strand | O94953 |
| B | Lysine-specific demethylase 4B (EC 1.14.11.66) | protein | 339 | 27% helix, 24% strand | O94953 |
Ligands and binding sites
- 9DJ · 3-[({(1R)-6-[methyl(phenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl}methyl)amino]pyridine-4-carboxylic acid · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.67 | 0.83 | 34 | NI, 9DJ |
| 2 | 251 | 0.66 | 0.83 | 34 | NI, 9DJ |
| 3 | 185 | 0.56 | 0.79 | 27 | empty |
| 4 | 152 | 0.51 | 0.79 | 26 | empty |
| 5 | 171 | 0.46 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 415 Ų buried · 7 hydrogen bonds · protein-protein
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 O94953
- Elsewhere: RCSB PDB 7JM5 · PDBe 7JM5 · UniProt O94953
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