MolNFT v2 · #157768 · protein
Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-pyrimidi 1 SHP389
6MDC · Tyrosine-protein phosphatase non-receptor type 11: “Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-pyrimidi 1 SHP389”. X-ray diffraction at 2.14, 2 ligands (JEA, PO4), 13 pockets (best…
- PDB
- 6MDC
- Type
- protein
- Length
- 953 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.14
- Source
- Homo sapiens
- Molecule
- Tyrosine-protein phosphatase non-receptor type 11
- EC
- 3.1.3.48
- UniProt
- Q06124
- Ligands
- JEA, PO4
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.14 · 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 | 483 | 30% helix, 27% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 470 | 32% helix, 27% strand | Q06124 |
Ligands and binding sites
- JEA · 6-[(3S,4S)-4-amino-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl]-3-[3-chloro-2-(cyclopropylamino)pyridin-4-yl]-5-methyl-2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 5 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.68 | 0.81 | 35 | JEA |
| 2 | 757 | 0.67 | 0.75 | 60 | empty |
| 3 | 435 | 0.67 | 0.79 | 39 | JEA |
| 4 | 119 | 0.51 | 0.81 | 23 | empty |
| 5 | 117 | 0.51 | 0.81 | 24 | PO4 |
Interfaces
1 interface between chains.
- A–B · 166 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6MDC · 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
- Q06124 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type 11… · a predicted model of the same protein · chain B 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 6MDC · PDBe 6MDC · UniProt Q06124
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