Research workbench
Structure of human SHP2 in complex with compound 22
Analyse Structure of human SHP2 in complex with compound 22 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R7D
- Type
- protein
- Length
- 984 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
- 37I
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 489 | 30% helix, 25% strand | Q06124 |
| B | Tyrosine-protein phosphatase non-receptor type 11 (EC 3.1.3.48) | protein | 495 | 31% helix, 25% strand | Q06124 |
Ligands and binding sites
- 37I · 4-[6-(4-amino-4-methylpiperidin-1-yl)-1H-pyrazolo[3,4-b]pyrazin-3-yl]-3-chloro-N-methylpyridin-2-amine · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.83 | 0.85 | 97 | PG4 |
| 2 | 513 | 0.67 | 0.78 | 52 | 37I |
| 3 | 442 | 0.65 | 0.78 | 38 | 37I |
| 4 | 125 | 0.48 | 0.79 | 26 | empty |
| 5 | 118 | 0.41 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 793 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7R7D · Structure of human SHP2 in complex with compound 22 · 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 7R7D · PDBe 7R7D · UniProt Q06124
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