Research workbench
Wildtype PTP1b in complex with DES5743
Analyse Wildtype PTP1b in complex with DES5743 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8G69
- Type
- protein
- Length
- 585 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.53
- Source
- Homo sapiens
- Molecule
- Tyrosine-protein phosphatase non-receptor type 1
- EC
- 3.1.3.48
- UniProt
- P18031
- Ligands
- YXN, MG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.53 · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 1 (EC 3.1.3.48) | protein | 298 | 34% helix, 21% strand | P18031 |
| B | Tyrosine-protein phosphatase non-receptor type 1 (EC 3.1.3.48) | protein | 287 | 34% helix, 22% strand | P18031 |
Ligands and binding sites
- YXN · 4-(5-ethyl-3-methyl-1H-pyrazol-1-yl)aniline · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains 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 | 632 | 0.69 | 0.77 | 56 | YXN |
| 2 | 150 | 0.47 | 0.77 | 22 | empty |
| 3 | 145 | 0.45 | 0.76 | 22 | empty |
| 4 | 99 | 0.33 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 613 Ų buried · 2 hydrogen bonds · protein-protein
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 P18031
- Elsewhere: RCSB PDB 8G69 · PDBe 8G69 · UniProt P18031
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