MolNFT v1 · #144215 · protein
Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitors SHP099 and SHP504
6BMW · Tyrosine-protein phosphatase non-receptor type 11: “Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitors SHP099 and SHP504”. X-ray diffraction, 3 ligands (5OD, DZS, PO4), 12 pockets (best druggability…
- PDB
- 6BMW
- 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
- 5OD, DZS, PO4
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 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 | 475 | 30% helix, 26% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 473 | 31% helix, 27% strand | Q06124 |
Ligands and binding sites
- 5OD · 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine · ligand · 2 copies · chains A, B
- DZS · 3-{4-[(2-chlorophenyl)methyl]-5-oxo-4,5-dihydro[1,2, 4]triazolo[4,3-a]quinazolin-1-yl}-4-hydroxybenzoic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.67 | 0.75 | 62 | empty |
| 2 | 468 | 0.65 | 0.78 | 32 | 5OD |
| 3 | 408 | 0.64 | 0.78 | 34 | 5OD |
| 4 | 123 | 0.56 | 0.83 | 23 | PO4 |
| 5 | 104 | 0.45 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 168 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6BMW · Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors… · 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 6BMW · PDBe 6BMW · UniProt Q06124
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