Research workbench
Crystal structure of small molecule vinylsulfonamide 8 covalently bound to K-RAS G12C
Analyse Crystal structure of small molecule vinylsulfonamide 8 covalently bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LYF
- Type
- protein
- Length
- 473 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GDP, 21C
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 161 | 39% helix, 27% strand | P01116 |
| B | GTPase KRAS | protein | 158 | 39% helix, 24% strand | P01116 |
| C | GTPase KRAS | protein | 154 | 38% helix, 25% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- 21C · N-{1-[N-(4,5-dichloro-2-hydroxyphenyl)glycyl]piperidin-4-yl}ethanesulfonamide · ligand · chains B
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 | 727 | 0.68 | 0.76 | 54 | empty |
| 2 | 279 | 0.62 | 0.80 | 33 | empty |
| 3 | 104 | 0.53 | 0.83 | 19 | 21C |
| 4 | 83 | 0.45 | 0.80 | 17 | empty |
| 5 | 66 | 0.43 | 0.82 | 22 | empty |
Interfaces
2 interfaces between chains.
- B–C · 267 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 263 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4LYF · Crystal Structure of small molecule vinylsulfonamide 8 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 4LYF · PDBe 4LYF · UniProt P01116
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