Research workbench
Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric inhibitor rmc-4550
Analyse Non-receptor protein tyrosine phosphatase SHP2 in complex with allosteric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RCT
- Type
- protein
- Length
- 991 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
- 4Q4, CL
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 501 | 30% helix, 26% strand | Q06124 |
| A | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 490 | 31% helix, 26% strand | Q06124 |
Ligands and binding sites
- 4Q4 · {3-[(3S,4S)-4-amino-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl]-6-(2,3-dichlorophenyl)-5-methylpyrazin-2-yl}methanol · ligand · 2 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.69 | 0.80 | 39 | 4Q4 |
| 2 | 689 | 0.66 | 0.75 | 62 | empty |
| 3 | 416 | 0.65 | 0.78 | 37 | 4Q4, CL |
| 4 | 103 | 0.52 | 0.83 | 24 | empty |
| 5 | 243 | 0.49 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- B–A · 190 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7RCT · Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor… · the same entry in another collection · chain B against B, 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 7RCT · PDBe 7RCT · UniProt Q06124
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