Research workbench
Structure of human SHP2 in complex with compound 27
Analyse Structure of human SHP2 in complex with compound 27 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R7I
- Type
- protein
- Length
- 977 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.85
- Source
- Homo sapiens
- Molecule
- Tyrosine-protein phosphatase non-receptor type 11
- EC
- 3.1.3.48
- UniProt
- Q06124
- Ligands
- 3CW
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.85 · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 489 | 29% helix, 25% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 488 | 30% helix, 25% strand | Q06124 |
Ligands and binding sites
- 3CW · [3-(4-amino-4-methylpiperidin-1-yl)-6-(2,3-dichlorophenyl)-5-methylpyrazin-2-yl]methanol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.78 | 0.80 | 92 | empty |
| 2 | 484 | 0.68 | 0.79 | 58 | 3CW |
| 3 | 415 | 0.65 | 0.79 | 36 | 3CW |
| 4 | 171 | 0.61 | 0.84 | 28 | empty |
| 5 | 117 | 0.50 | 0.80 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 731 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7R7I · Structure of human SHP2 in complex with compound 27 · the same entry in another collection · chain A against A, TM-score 1.00
- Q06124 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type 11… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 7R7I · PDBe 7R7I · UniProt Q06124
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