Research workbench
RAS guanine nucleotide exchange factor SOS1 (rem-CDC25) in complex with small molecule inhibitor compound 17
Analyse RAS guanine nucleotide exchange factor SOS1 (rem-CDC25) in complex with small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OVF
- Type
- protein
- Length
- 472 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Son of sevenless homolog 1
- UniProt
- Q07889
- Ligands
- AWT
- Pockets
- 7 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Son of sevenless homolog 1 | protein | 472 | 60% helix, 4% strand | Q07889 |
Ligands and binding sites
- AWT · 6,7-dimethoxy-2-methyl-~{N}-[(1~{R})-1-[3-(1~{H}-pyrazol-4-yl)phenyl]ethyl]quinazolin-4-amine · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.44 | 0.77 | 21 | empty |
| 2 | 106 | 0.41 | 0.77 | 26 | empty |
| 3 | 88 | 0.41 | 0.78 | 10 | AWT |
| 4 | 126 | 0.39 | 0.74 | 30 | empty |
| 5 | 53 | 0.35 | 0.78 | 15 | empty |
Compared structures
- 5OVF · 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 5OVF · PDBe 5OVF · UniProt Q07889
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