MolNFT v1 · #129808 · protein
RAS guanine nucleotide exchange factor SOS1 (rem-CDC25) in complex with small molecule inhibitor bay-293 (compound 23)
5OVI · Son of sevenless homolog 1: “RAS guanine nucleotide exchange factor SOS1 (rem-CDC25) in complex with small molecule inhibitor bay-293…”. X-ray diffraction, 1 ligand (AXH), 6 pockets (best druggability 0.54). MolNFT v1 #129808 on…
- PDB
- 5OVI
- Type
- protein
- Length
- 466 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Son of sevenless homolog 1
- UniProt
- Q07889
- Ligands
- AXH
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Son of sevenless homolog 1 | protein | 466 | 59% helix, 4% strand | Q07889 |
Ligands and binding sites
- AXH · 6,7-dimethoxy-2-methyl-~{N}-[(1~{R})-1-[4-[2-(methylaminomethyl)phenyl]thiophen-2-yl]ethyl]quinazolin-4-amine · ligand · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.54 | 0.84 | 16 | AXH |
| 2 | 122 | 0.42 | 0.76 | 25 | empty |
| 3 | 133 | 0.41 | 0.75 | 22 | empty |
| 4 | 61 | 0.35 | 0.77 | 17 | EDO |
| 5 | 58 | 0.30 | 0.75 | 17 | empty |
Compared structures
- 5OVI · Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in complex with small molecule… · 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 A against A, TM-score 0.96
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 Q07889
- Elsewhere: RCSB PDB 5OVI · PDBe 5OVI · UniProt Q07889
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