MolNFT v1 · #144214 · protein
Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor SHP504
6BMV · Tyrosine-protein phosphatase non-receptor type 11: “Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor SHP504”. X-ray diffraction, 2 ligands (DZS, PO4), 12 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 6BMV
- Type
- protein
- Length
- 964 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
- DZS, PO4
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 30% 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 | 483 | 30% helix, 26% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 481 | 31% helix, 26% strand | Q06124 |
Ligands and binding sites
- 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.70 | 0.75 | 80 | empty |
| 2 | 406 | 0.62 | 0.77 | 34 | empty |
| 3 | 363 | 0.62 | 0.78 | 32 | empty |
| 4 | 139 | 0.55 | 0.82 | 26 | empty |
| 5 | 93 | 0.51 | 0.83 | 23 | PO4 |
Interfaces
1 interface between chains.
- A–B · 161 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6BMV · Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP504 · 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 6BMV · PDBe 6BMV · UniProt Q06124
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