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Crystal structure of human KDM4 with small molecule inhibitor QC5714
Analyse Crystal structure of human KDM4 with small molecule inhibitor QC5714 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VMP
- Type
- protein
- Length
- 1,370 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- 9FJ, NI, ZN
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 347 | 31% helix, 24% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 335 | 32% helix, 25% strand | O75164 |
| D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 341 | 31% helix, 25% strand | O75164 |
Ligands and binding sites
- 9FJ · 3-({[(1R)-6-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]methyl}amino)pyridine-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.71 | 0.83 | 40 | NI, 9FJ |
| 2 | 379 | 0.70 | 0.82 | 43 | NI, 9FJ |
| 3 | 368 | 0.70 | 0.82 | 36 | NI, 9FJ |
| 4 | 381 | 0.69 | 0.82 | 41 | NI, 9FJ |
| 5 | 465 | 0.63 | 0.76 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–B · 551 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 548 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 369 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5VMP · Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714 · 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 O75164
- Elsewhere: RCSB PDB 5VMP · PDBe 5VMP · UniProt O75164
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