MolNFT v1 · #160043 · protein
Crystal structure of human KRAS G12C covalently bound to an acryloylazetidine acetamide inhibitor.
6P8X · GTPase KRAS: “Crystal structure of human KRAS G12C covalently bound to an acryloylazetidine acetamide inhibitor.”. X-ray diffraction, 3 ligands (GDP, O5V, CA), 3 pockets (best druggability 0.84). MolNFT v1 #160043 on GenesisL1: 3D…
- PDB
- 6P8X
- Type
- protein
- Length
- 666 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GDP, O5V, CA
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GTPase KRAS | protein | 166 | 37% helix, 25% strand | P01116 |
| C, D | GTPase KRAS | protein | 167 | 37% helix, 25% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- O5V · 2-[4-bromo-2-(3-phenyl-2,5-dihydro-1H-pyrrole-1-carbonyl)phenoxy]-N-(1-propanoylazetidin-3-yl) acetamide · ligand · 4 copies · chains A, D, B, C
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.84 | 0.85 | 112 | CA, GDP, O5V |
| 2 | 991 | 0.82 | 0.84 | 105 | CA, GDP, O5V |
| 3 | 202 | 0.51 | 0.77 | 31 | empty |
Interfaces
4 interfaces between chains.
- A–D · 495 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 493 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 260 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 217 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6P8X · Crystal structure of human KRAS G12C covalently bound to an acryloylazetidine acetamide… · 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 6P8X · PDBe 6P8X · UniProt P01116
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