Research workbench
Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor isoxazolo-pyridinone 3
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
- 6MD9
- Type
- protein
- Length
- 938 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
- JEJ, PO4
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 31% 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 | 468 | 31% helix, 27% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 470 | 31% helix, 27% strand | Q06124 |
Ligands and binding sites
- JEJ · 3-(2-chlorophenyl)-6-{4-[(dimethylamino)methyl]phenyl}-5-methyl[1,2]oxazolo[4,5-c]pyridin-4(5H)-one · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.69 | 0.76 | 64 | empty |
| 2 | 407 | 0.66 | 0.79 | 30 | JEJ |
| 3 | 372 | 0.65 | 0.80 | 35 | JEJ |
| 4 | 120 | 0.52 | 0.82 | 23 | PO4 |
| 5 | 90 | 0.45 | 0.80 | 16 | PO4 |
Interfaces
1 interface between chains.
- A–B · 168 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6MD9 · NON-RECEPTOR PROTEIN TYROSINE PHOSPHATASE SHP2 IN COMPLEX WITH ALLOSTERIC INHIBITOR… · 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 6MD9 · PDBe 6MD9 · UniProt Q06124
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