MolNFT v1 · #99269 · protein
Crystal structure of small molecule vinylsulfonamide 9 covalently bound to K-RAS G12C
4LYH · GTPase KRAS: “Crystal structure of small molecule vinylsulfonamide 9 covalently bound to K-RAS G12C”. X-ray diffraction, 3 ligands (GDP, 21F, SO4), 6 pockets (best druggability 0.71). MolNFT v1 #99269 on GenesisL1: 3D structure…
- PDB
- 4LYH
- Type
- protein
- Length
- 478 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GDP, 21F, SO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 163 | 39% helix, 25% strand | P01116 |
| B | GTPase KRAS | protein | 159 | 41% helix, 23% strand | P01116 |
| C | GTPase KRAS | protein | 156 | 41% helix, 26% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- 21F · N-{1-[N-(4-chloro-5-iodo-2-methoxyphenyl)glycyl]piperidin-4-yl}ethanesulfonamide · ligand · 2 copies · chains B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.71 | 0.78 | 60 | empty |
| 2 | 337 | 0.64 | 0.80 | 33 | empty |
| 3 | 111 | 0.58 | 0.85 | 15 | 21F |
| 4 | 73 | 0.47 | 0.83 | 14 | empty |
| 5 | 93 | 0.40 | 0.77 | 20 | 21F |
Interfaces
2 interfaces between chains.
- A–B · 403 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 265 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4LYH · Crystal Structure of small molecule vinylsulfonamide 9 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 4LYH · PDBe 4LYH · UniProt P01116
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