Research workbench
Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods
Analyse Expanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V9N
- Type
- protein
- Length
- 802 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.648
- Source
- Homo sapiens
- Molecule
- GTPase HRas; Son of sevenless homolog 1
- UniProt
- P01112, Q07889
- Ligands
- GNP, QTD, MG, NA
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.648 · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase HRas | protein | 166 | 37% helix, 27% strand | P01112 |
| B | Son of sevenless homolog 1 | protein | 469 | 59% helix, 4% strand | Q07889 |
| C | GTPase HRas | protein | 167 | 34% helix, 26% strand | P01112 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- QTD · 4-phenoxybenzene-1-sulfonamide · ligand · chains B
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains C
- FMT · Formic acid · additive · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.79 | 0.82 | 100 | GNP, MG |
| 2 | 255 | 0.72 | 0.87 | 44 | empty |
| 3 | 51 | 0.69 | 0.97 | 25 | FMT |
| 4 | 277 | 0.63 | 0.81 | 45 | empty |
| 5 | 130 | 0.58 | 0.83 | 20 | QTD |
Interfaces
2 interfaces between chains.
- B–C · 1794 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1578 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6V9N · Expanding the chemical landscape of SOS1 activators using fragment based methods · the same entry in another collection · chain A against A, TM-score 1.00
- Q07889 · AlphaFold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P01112
- Every structure of UniProt Q07889
- Elsewhere: RCSB PDB 6V9N · PDBe 6V9N · UniProt P01112 · UniProt Q07889
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