MolNFT v1 · #146031 · protein
RAS:SOS:RAS in complex with a small molecule activator
6D5G · GTPase HRAS: “RAS:SOS:RAS in complex with a small molecule activator”. X-ray diffraction, 4 ligands (GNP, FVD, MG), 12 pockets (best druggability 0.78). MolNFT v1 #146031 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6D5G
- Type
- protein
- Length
- 802 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS; Son of sevenless homolog 1
- UniProt
- P01112, Q07889
- Ligands
- GNP, FVD, MG, CL
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 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
- FVD · 6-chloro-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-4-(1,2,3,6-tetrahydropyridin-4-yl)-1H-benzimidazole · ligand · chains B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- FMT · Formic acid · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains B
- BME · Beta-mercaptoethanol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.78 | 0.80 | 101 | GNP, MG, CL |
| 2 | 57 | 0.68 | 0.96 | 15 | empty |
| 3 | 194 | 0.68 | 0.86 | 35 | empty |
| 4 | 220 | 0.60 | 0.81 | 41 | empty |
| 5 | 148 | 0.58 | 0.82 | 19 | FVD, GOL |
Interfaces
2 interfaces between chains.
- B–C · 1817 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1565 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
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 6D5G · PDBe 6D5G · UniProt P01112 · UniProt Q07889
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