MolNFT v1 · #99385 · protein
Crystal structure of small molecule vinylsulfonamide covalently bound to K-RAS G12C
4M1W · K-RAS GTPase: “Crystal structure of small molecule vinylsulfonamide covalently bound to K-RAS G12C”. X-ray diffraction, 3 ligands (21R, GDP, MG), 6 pockets (best druggability 0.67). MolNFT v1 #99385 on GenesisL1: 3D structure…
- PDB
- 4M1W
- Type
- protein
- Length
- 476 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- K-RAS GTPase
- UniProt
- P01116
- Ligands
- 21R, GDP, MG
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | K-RAS GTPase | protein | 160 | 39% helix, 26% strand | P01116 |
| B | K-RAS GTPase | protein | 159 | 40% helix, 24% strand | P01116 |
| C | K-RAS GTPase | protein | 157 | 42% helix, 26% strand | P01116 |
Ligands and binding sites
- 21R · N-{1-[N-(4,5-dichloro-2-ethylphenyl)glycyl]piperidin-4-yl}ethanesulfonamide · ligand · 3 copies · chains A, B, C
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.67 | 0.77 | 56 | empty |
| 2 | 347 | 0.65 | 0.80 | 30 | empty |
| 3 | 100 | 0.58 | 0.86 | 13 | 21R |
| 4 | 136 | 0.53 | 0.81 | 21 | 21R |
| 5 | 65 | 0.44 | 0.82 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 307 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 265 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4M1W · Crystal Structure of small molecule vinylsulfonamide 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 4M1W · PDBe 4M1W · UniProt P01116
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