Research workbench
Crystal structure of KDM5A in complex with a naphthyridone inhibitor
Analyse Crystal structure of KDM5A in complex with a naphthyridone inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K4L
- Type
- protein
- Length
- 1,174 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5A; Unknown peptide
- EC
- 1.14.11.-
- UniProt
- P29375
- Ligands
- 6QN, ZN, NI
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine-specific demethylase 5A (EC 1.14.11.-) | protein | 577 | 41% helix, 14% strand | P29375 |
| F, G | Unknown peptide | protein | 10 | 40% helix, 0% strand | — |
Ligands and binding sites
- 6QN · ~{N}-ethyl-4-oxidanyl-2-oxidanylidene-1~{H}-1,7-naphthyridine-3-carboxamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.79 | 0.81 | 89 | NI, 6QN |
| 2 | 1160 | 0.79 | 0.80 | 93 | 6QN |
| 3 | 149 | 0.74 | 0.92 | 25 | empty |
| 4 | 135 | 0.73 | 0.92 | 24 | empty |
| 5 | 516 | 0.70 | 0.79 | 55 | empty |
Interfaces
5 interfaces between chains.
- A–B · 725 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 310 Ų buried · 7 hydrogen bonds · protein-protein
- A–G · 283 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 157 Ų buried · 1 hydrogen bond · protein-protein
- B–G · 148 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5K4L · Crystal structure of KDM5A in complex with a naphthyridone inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P29375 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5A (P29375) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P29375
- Elsewhere: RCSB PDB 5K4L · PDBe 5K4L · UniProt P29375
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