Research workbench
Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor tk-453
Analyse Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VXG
- Type
- protein
- Length
- 1,925 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type 11
- EC
- 3.1.3.48
- UniProt
- Q06124
- Ligands
- 83Q
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 477 | 30% helix, 26% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 480 | 30% helix, 26% strand | Q06124 |
| C | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 481 | 30% helix, 26% strand | Q06124 |
| D | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 487 | 29% helix, 26% strand | Q06124 |
Ligands and binding sites
- 83Q · 6-[4-(aminomethyl)-4-methyl-piperidin-1-yl]-3-[2,3-bis(chloranyl)phenyl]sulfanyl-pyrazin-2-amine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.72 | 0.76 | 94 | empty |
| 2 | 883 | 0.71 | 0.76 | 86 | empty |
| 3 | 752 | 0.68 | 0.75 | 58 | empty |
| 4 | 327 | 0.62 | 0.79 | 27 | 83Q |
| 5 | 280 | 0.62 | 0.80 | 28 | 83Q |
Interfaces
3 interfaces between chains.
- A–D · 658 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 191 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 170 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7VXG · Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor TK-453 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q06124
- Elsewhere: RCSB PDB 7VXG · PDBe 7VXG · UniProt Q06124
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