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Structure of histone lysine demethylase KDM5A in complex with selective inhibitor
Analyse Structure of histone lysine demethylase KDM5A in complex with selective… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CEH
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- 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
- 50P, ZN, NI
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5A (EC 1.14.11.-) | protein | 577 | 42% helix, 13% strand | P29375 |
| B | Unknown peptide | protein | 10 | 40% helix, 0% strand | — |
Ligands and binding sites
- 50P · 7-oxo-5-phenyl-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.79 | 0.80 | 89 | NI, 50P |
| 2 | 132 | 0.73 | 0.93 | 25 | empty |
| 3 | 72 | 0.58 | 0.89 | 16 | empty |
| 4 | 76 | 0.54 | 0.85 | 18 | empty |
| 5 | 54 | 0.42 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 151 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5CEH · Structure of histone lysine demethylase KDM5A in complex with selective 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 5CEH · PDBe 5CEH · UniProt P29375
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