MolNFT v1 · #147851 · protein
RAS guanine nucleotide exchange factor SOS1 (rem-CDC25) in complex with KRAS(G12C) and fragment screening hit F1
6EPM · GTPase KRAS: “RAS guanine nucleotide exchange factor SOS1 (rem-CDC25) in complex with KRAS(G12C) and fragment screening hit…”. X-ray diffraction, 1 ligand (BQ5), 7 pockets (best druggability 0.71). MolNFT v1 #147851 on GenesisL1: 3D…
- PDB
- 6EPM
- Type
- protein
- Length
- 631 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
- BQ5
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | GTPase KRAS | protein | 169 | 41% helix, 25% strand | P01116 |
| S | Son of sevenless homolog 1 | protein | 462 | 58% helix, 5% strand | Q07889 |
Ligands and binding sites
- BQ5 · (1-phenyl-5,6-dihydro-4~{H}-cyclopenta[c]pyrazol-3-yl) methanamine · 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.71 | 0.82 | 63 | GOL |
| 2 | 283 | 0.70 | 0.84 | 49 | empty |
| 3 | 107 | 0.55 | 0.83 | 15 | BQ5 |
| 4 | 168 | 0.46 | 0.76 | 30 | empty |
| 5 | 143 | 0.46 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- R–S · 1761 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6EPM · Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in complex with KRAS(G12C) and… · 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 6EPM · PDBe 6EPM · UniProt P01116 · UniProt Q07889
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