MolNFT v1 · #156722 · protein
Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor pyrazolo-pyrimidinone 5
6MDB · Tyrosine-protein phosphatase non-receptor type 11: “Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor pyrazolo-pyrimidinone 5”. X-ray diffraction, 2 ligands (JE4, PO4), 13 pockets (best druggability…
- PDB
- 6MDB
- Type
- protein
- Length
- 968 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
- JE4, PO4
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 29% 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 | 487 | 29% helix, 27% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 481 | 30% helix, 26% strand | Q06124 |
Ligands and binding sites
- JE4 · 6-(4-amino-4-methylpiperidin-1-yl)-3-(2,3-dichlorophenyl)-5-methyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-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
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.69 | 0.75 | 58 | empty |
| 2 | 330 | 0.66 | 0.81 | 28 | JE4 |
| 3 | 420 | 0.65 | 0.78 | 35 | JE4 |
| 4 | 118 | 0.50 | 0.81 | 20 | empty |
| 5 | 112 | 0.48 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 170 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6MDB · 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 6MDB · PDBe 6MDB · UniProt Q06124
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