MolNFT v1 · #95931 · protein
Cyrstal structure of protein tyrosine phosphatase lyp catalytic domain complex with small molecular inhibitor L75N04
4J51 · Tyrosine-protein phosphatase non-receptor type 22: “Cyrstal structure of protein tyrosine phosphatase lyp catalytic domain complex with small molecular inhibitor…”. X-ray diffraction, 1 ligand (N75), 8 pockets (best druggability…
- 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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