MolNFT v1 · #160310 · protein
Crystal structure of human KRAS G12C covalently bound to a quinazolinone inhibitor
6PGP · GTPase KRAS: “Crystal structure of human KRAS G12C covalently bound to a quinazolinone inhibitor”. X-ray diffraction, 3 ligands (GDP, OHY, CA), 5 pockets (best druggability 0.65). MolNFT v1 #160310 on GenesisL1: 3D structure…
- PDB
- 6PGP
- Type
- protein
- Length
- 338 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GDP, OHY, CA
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GTPase KRAS | protein | 169 | 38% helix, 25% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- OHY · 6-chloro-7-(2-fluoro-6-hydroxyphenyl)-4-(4-propanoylpiperazin-1-yl)-1-[2-(propan-2-yl) phenyl]quinazolin-2(1H)-one · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.65 | 0.80 | 47 | GDP, CA, OHY |
| 2 | 361 | 0.65 | 0.79 | 46 | GDP, CA, OHY |
| 3 | 153 | 0.60 | 0.84 | 26 | empty |
| 4 | 157 | 0.52 | 0.79 | 26 | empty |
| 5 | 54 | 0.31 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 482 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6PGP · Crystal structure of human KRAS G12C covalently bound to a quinazoli inhibitor · 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 6PGP · PDBe 6PGP · UniProt P01116
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