Research workbench
Vascular endothelial protein tyrosine phosphatase in complex with Cpd-2
Analyse Vascular endothelial protein tyrosine phosphatase in complex with Cpd-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8JBY
- Type
- protein
- Length
- 559 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.99
- Source
- Homo sapiens
- Molecule
- Receptor-type tyrosine-protein phosphatase beta
- EC
- 3.1.3.48
- UniProt
- P23467
- Ligands
- U7L
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.99 · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-type tyrosine-protein phosphatase beta (EC 3.1.3.48) | protein | 287 | 35% helix, 21% strand | P23467 |
| B | Receptor-type tyrosine-protein phosphatase beta (EC 3.1.3.48) | protein | 272 | 37% helix, 21% strand | P23467 |
Ligands and binding sites
- U7L · 4-(hydroxymethyl)-5-(1-methylindol-3-yl)-1,2-oxazole-3-carboxylic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.72 | 0.77 | 97 | EDO, U7L |
| 2 | 65 | 0.39 | 0.79 | 18 | empty |
| 3 | 54 | 0.35 | 0.79 | 14 | U7L |
| 4 | 52 | 0.34 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 632 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- P23467 · AlphaFold monomer V2.0 prediction for receptor-type tyrosine-protein phosphatase beta… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P23467
- Elsewhere: RCSB PDB 8JBY · PDBe 8JBY · UniProt P23467
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