MolNFT v1 · #149624 · protein
Crystal structure of KDM4A with compound yp-03-038
6G5W · Lysine-specific demethylase 4A: “Crystal structure of KDM4A with compound yp-03-038”. X-ray diffraction, 4 ligands (ENZ, NI, ZN), 9 pockets (best druggability 0.71). MolNFT v1 #149624 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6G5W
- Type
- protein
- Length
- 692 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
- ENZ, NI, ZN, NA
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 349 | 30% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 343 | 30% helix, 24% strand | O75164 |
Ligands and binding sites
- ENZ · (4~{R})-5-methyl-4-phenyl-2-pyridin-2-yl-pyrazolidin-3-one · ligand · chains A, B
- NI · Nickel (II) ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- CIT · Citric acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.71 | 0.77 | 83 | NI, EDO, CIT, ENZ |
| 2 | 347 | 0.71 | 0.83 | 38 | NI, CIT |
| 3 | 353 | 0.69 | 0.82 | 40 | NI, CIT |
| 4 | 73 | 0.49 | 0.84 | 19 | empty |
| 5 | 155 | 0.42 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 426 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6G5W · Crystal Structure of KDM4A with compound YP-03-038 · 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 6G5W · PDBe 6G5W · UniProt O75164
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