MolNFT v1 · #156724 · protein
Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor imidazo-pyridine 24
6MDD · Tyrosine-protein phosphatase non-receptor type 11: “Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor imidazo-pyridine 24”. X-ray diffraction, 2 ligands (JE7, PO4), 11 pockets (best druggability…
- PDB
- 6MDD
- Type
- protein
- Length
- 948 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
- JE7, PO4
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 31% 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 | 477 | 31% helix, 27% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 471 | 32% helix, 25% strand | Q06124 |
Ligands and binding sites
- JE7 · 5-[(2,3-dichlorophenyl)sulfanyl]-3H-imidazo[4,5-b]pyridin-2-amine · 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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.69 | 0.76 | 58 | empty |
| 2 | 478 | 0.65 | 0.78 | 46 | JE7 |
| 3 | 374 | 0.62 | 0.78 | 35 | JE7 |
| 4 | 151 | 0.54 | 0.81 | 23 | empty |
| 5 | 63 | 0.40 | 0.79 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 163 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6MDD · 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 6MDD · PDBe 6MDD · UniProt Q06124
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