Research workbench
Crystal structure of small molecule acrylamide 16 covalently bound to K-RAS G12C
Analyse Crystal structure of small molecule acrylamide 16 covalently bound to K-RAS G12C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M22
- Type
- protein
- Length
- 485 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- K-RAS GTPase
- UniProt
- P01116
- Ligands
- GDP, 22C, MG
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | K-RAS GTPase | protein | 160 | 37% helix, 27% strand | P01116 |
| B | K-RAS GTPase | protein | 166 | 39% helix, 24% strand | P01116 |
| C | K-RAS GTPase | protein | 159 | 39% helix, 25% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- 22C · 1-{4-[(2,4-dichlorophenoxy)acetyl]piperazin-1-yl}propan-1-one · ligand · 2 copies · chains B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.74 | 0.77 | 104 | MG, 22C, GDP |
| 2 | 214 | 0.57 | 0.79 | 42 | MG, 22C, GDP |
| 3 | 141 | 0.52 | 0.80 | 28 | MG, GDP |
Interfaces
3 interfaces between chains.
- B–C · 313 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 261 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 215 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4M22 · Crystal Structure of small molecule acrylamide 16 covalently bound to K-Ras G12C · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 4M22 · PDBe 4M22 · UniProt P01116
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.