Research workbench
Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitors SHP099 and SHP844
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
- 6BMY
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- 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
- 5OD, DYV, PO4
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 480 | 30% helix, 28% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 474 | 30% helix, 27% strand | Q06124 |
Ligands and binding sites
- 5OD · 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine · ligand · 2 copies · chains A, B
- DYV · 1-(3-chloro-4-{[1-(2-hydroxy-3-methoxyphenyl)-5-oxo[1, 2,4]triazolo[4,3-a]quinazolin-4(5H)-yl]methyl}benzene-1-carbonyl)-L-proline · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.68 | 0.75 | 61 | empty |
| 2 | 394 | 0.65 | 0.79 | 36 | 5OD |
| 3 | 336 | 0.63 | 0.79 | 28 | 5OD |
| 4 | 71 | 0.52 | 0.86 | 17 | empty |
| 5 | 99 | 0.49 | 0.82 | 19 | GOL |
Interfaces
1 interface between chains.
- A–B · 172 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6BMY · Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors… · 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 6BMY · PDBe 6BMY · UniProt Q06124
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