MolNFT v1 · #137176 · protein
Crystal structure of KDM4 with the small molecule inhibitor QC6352
5VGI · Lysine-specific demethylase 4A: “Crystal structure of KDM4 with the small molecule inhibitor QC6352”. X-ray diffraction, 3 ligands (9DJ, NI, ZN), 15 pockets (best druggability 0.77). MolNFT v1 #137176 on GenesisL1: 3D structure…
- PDB
- 5VGI
- Type
- protein
- Length
- 1,372 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
- 9DJ, NI, ZN
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 345 | 30% helix, 24% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 337 | 31% helix, 25% strand | O75164 |
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 · 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
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.77 | 0.79 | 83 | NI, 9DJ |
| 2 | 416 | 0.72 | 0.83 | 41 | NI, 9DJ |
| 3 | 401 | 0.71 | 0.82 | 39 | NI, 9DJ |
| 4 | 389 | 0.71 | 0.82 | 41 | NI, 9DJ |
| 5 | 528 | 0.62 | 0.74 | 54 | empty |
Interfaces
3 interfaces between chains.
- A–C · 601 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 184 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 155 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5VGI · Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 · 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 5VGI · PDBe 5VGI · UniProt O75164
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