MolNFT v1 · #156721 · protein
Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor pyrazolo-pyridine 4
6MDA · Tyrosine-protein phosphatase non-receptor type 11: “Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor pyrazolo-pyridine 4”. X-ray diffraction, 2 ligands (JED, PO4), 10 pockets (best druggability…
- PDB
- 6MDA
- 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
- JED, PO4
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 32% 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 | 468 | 32% helix, 27% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 470 | 31% helix, 26% strand | Q06124 |
Ligands and binding sites
- JED · 3-(4-bromophenyl)-6-(4-methylphenyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.67 | 0.82 | 31 | JED |
| 2 | 733 | 0.67 | 0.75 | 57 | empty |
| 3 | 387 | 0.64 | 0.79 | 37 | JED |
| 4 | 87 | 0.42 | 0.79 | 15 | empty |
| 5 | 104 | 0.42 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 157 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6MDA · 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 6MDA · PDBe 6MDA · UniProt Q06124
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