MolNFT v1 · #99381 · protein
Crystal structure of small molecule vinylsulfonamide 13 covalently bound to K-RAS G12C
4M1S · K-RAS GTPase: “Crystal structure of small molecule vinylsulfonamide 13 covalently bound to K-RAS G12C”. X-ray diffraction, 2 ligands (GDP, 21K), 2 pockets (best druggability 0.68). MolNFT v1 #99381 on GenesisL1: 3D structure…
- PDB
- 4M1S
- Type
- protein
- Length
- 468 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- K-RAS GTPase
- UniProt
- P01116
- Ligands
- GDP, 21K
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | K-RAS GTPase | protein | 161 | 39% helix, 26% strand | P01116 |
| B | K-RAS GTPase | protein | 159 | 39% helix, 24% strand | P01116 |
| C | K-RAS GTPase | protein | 148 | 39% helix, 27% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- 21K · N-{1-[N-(2,4-dichlorophenyl)glycyl]piperidin-4-yl}ethanesulfonamide · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.68 | 0.77 | 56 | empty |
| 2 | 516 | 0.68 | 0.78 | 54 | 21K |
Interfaces
2 interfaces between chains.
- A–B · 343 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 136 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4M1S · Crystal Structure of small molecule vinylsulfonamide 13 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 4M1S · PDBe 4M1S · UniProt P01116
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.