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Structural basis for an allosteric EYA2 phosphatase inhibitor
Analyse Structural basis for an allosteric EYA2 phosphatase inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZMA
- Type
- protein
- Length
- 758 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eyes absent homolog 2
- EC
- 3.1.3.48
- UniProt
- O00167
- Ligands
- 9FX
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Eyes absent homolog 2 (EC 3.1.3.48) | protein | 253 | 51% helix, 9% strand | O00167 |
| A | Eyes absent homolog 2 (EC 3.1.3.48) | protein | 255 | 54% helix, 11% strand | O00167 |
| C | Eyes absent homolog 2 (EC 3.1.3.48) | protein | 250 | 52% helix, 10% strand | O00167 |
Ligands and binding sites
- 9FX · 3-fluoro-N'-[(E)-{5-[(pyrimidin-2-yl)sulfanyl]furan-2-yl}methylidene]benzohydrazide · ligand · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.73 | 0.84 | 49 | 9FX |
| 2 | 268 | 0.69 | 0.84 | 47 | 9FX |
| 3 | 152 | 0.65 | 0.86 | 24 | 9FX |
| 4 | 82 | 0.43 | 0.79 | 18 | empty |
| 5 | 110 | 0.39 | 0.75 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–A · 564 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 47 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 O00167
- Elsewhere: RCSB PDB 5ZMA · PDBe 5ZMA · UniProt O00167
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