MolNFT v1 · #156718 · protein
Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor pyrimidinone 7
6MD7 · Tyrosine-protein phosphatase non-receptor type 11: “Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor pyrimidinone 7”. X-ray diffraction, 2 ligands (JE1, PO4), 15 pockets (best druggability 0.68).…
- PDB
- 6MD7
- Type
- protein
- Length
- 985 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
- JE1, PO4
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 31% 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 | 496 | 31% helix, 25% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 489 | 31% helix, 26% strand | Q06124 |
Ligands and binding sites
- JE1 · 2-[4-(aminomethyl)-4-methylpiperidin-1-yl]-5-{[2-(trifluoromethyl)pyridin-3-yl]sulfanyl}pyrimidin-4(3H)-one · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.68 | 0.75 | 60 | empty |
| 2 | 413 | 0.67 | 0.80 | 35 | JE1, PO4 |
| 3 | 441 | 0.66 | 0.79 | 39 | JE1, PO4 |
| 4 | 153 | 0.55 | 0.81 | 25 | PO4 |
| 5 | 100 | 0.50 | 0.82 | 20 | PO4 |
Interfaces
1 interface between chains.
- A–B · 168 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6MD7 · 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 6MD7 · PDBe 6MD7 · UniProt Q06124
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