Research workbench
RAS guanine exchange factor SOS1 (rem-CDC25) in complex with KRAS(G12C) and fragment screening hit F4
Analyse RAS guanine exchange factor SOS1 (rem-CDC25) in complex with KRAS(G12C) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EPP
- Type
- protein
- Length
- 627 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; Son of sevenless homolog 1
- UniProt
- P01116, Q07889
- Ligands
- BOQ
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | GTPase KRAS | protein | 168 | 38% helix, 25% strand | P01116 |
| S | Son of sevenless homolog 1 | protein | 459 | 59% helix, 5% strand | Q07889 |
Ligands and binding sites
- BOQ · ethyl 2-(aminomethyl)-5-~{tert}-butyl-furan-3-carboxylate · ligand · chains S
- GOL · Glycerol · additive · chains R, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.69 | 0.81 | 50 | GOL |
| 2 | 228 | 0.65 | 0.83 | 37 | empty |
| 3 | 350 | 0.58 | 0.76 | 54 | empty |
| 4 | 106 | 0.54 | 0.83 | 16 | BOQ |
| 5 | 70 | 0.53 | 0.86 | 17 | empty |
Interfaces
1 interface between chains.
- R–S · 1728 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6EPP · RAS guanine exchange factor SOS1 (rem-CDC25) in complex with KRAS(G12C) and fragment… · the same entry in another collection · chain R against R, 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 P01116
- Every structure of UniProt Q07889
- Elsewhere: RCSB PDB 6EPP · PDBe 6EPP · UniProt P01116 · UniProt Q07889
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