Research workbench
Crystal structure of KDM4A with compound yp-02-145
Analyse Crystal structure of KDM4A with compound yp-02-145 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G5X
- Type
- protein
- Length
- 695 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- MY7, NI, ZN
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 351 | 32% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 344 | 31% helix, 24% strand | O75164 |
Ligands and binding sites
- MY7 · 2-(3-methyl-5-oxidanylidene-4-phenyl-4~{H}-pyrazol-1-yl)-3~{H}-benzimidazole-5-carboxylic acid · ligand · chains A, B
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- CIT · Citric acid · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.71 | 0.83 | 40 | NI, CIT |
| 2 | 655 | 0.70 | 0.77 | 61 | NI, CIT, MY7 |
| 3 | 383 | 0.70 | 0.82 | 42 | NI, CIT |
| 4 | 93 | 0.55 | 0.85 | 22 | EDO |
| 5 | 105 | 0.53 | 0.83 | 25 | EDO |
Interfaces
1 interface between chains.
- A–B · 490 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6G5X · Crystal Structure of KDM4A with compound YP-02-145 · 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 6G5X · PDBe 6G5X · UniProt O75164
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