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Cyrstal structure of protein tyrosine phosphatase lyp catalytic domain complex with small molecular inhibitor L75N04
Analyse Cyrstal structure of protein tyrosine phosphatase lyp catalytic domain complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J51
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 22
- EC
- 3.1.3.48
- UniProt
- Q9Y2R2
- Ligands
- N75
- Pockets
- 8 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosine-protein phosphatase non-receptor type 22 (EC 3.1.3.48) | protein | 302 | 40% helix, 20% strand | Q9Y2R2 |
Ligands and binding sites
- N75 · 3-[(3-chlorophenyl)ethynyl]-2-{4-[2-(cyclopropylamino)-2-oxoethoxy]phenyl}-6-hydroxy-1-benzofuran-5-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.47 | 0.77 | 21 | empty |
| 2 | 121 | 0.43 | 0.76 | 23 | empty |
| 3 | 137 | 0.42 | 0.75 | 17 | empty |
| 4 | 102 | 0.42 | 0.77 | 26 | empty |
| 5 | 134 | 0.40 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 71 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4J51 · Cyrstal structure of protein tyrosine phosphatase Lyp catalytic domain complex with small… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y2R2 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type 22… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9Y2R2
- Elsewhere: RCSB PDB 4J51 · PDBe 4J51 · UniProt Q9Y2R2
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