Research workbench
Crystal structure of human KRAS G12C covalently bound to a phthalazine inhibitor
Analyse Crystal structure of human KRAS G12C covalently bound to a phthalazine inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PGO
- Type
- protein
- Length
- 312 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GDP, OJ1, MG
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 160 | 36% helix, 26% strand | P01116 |
| B | GTPase KRAS | protein | 152 | 39% helix, 26% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- OJ1 · 1-{4-[7-chloro-6-(2-fluoro-6-hydroxyphenyl)-4-phenylphthalazin-1-yl]piperazin-1-yl}propan-1-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.56 | 0.77 | 38 | MG, GDP, OJ1 |
| 2 | 216 | 0.55 | 0.79 | 32 | empty |
| 3 | 61 | 0.34 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 580 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6PGO · Crystal structure of human KRAS G12C covalently bound to a phthalazine 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 6PGO · PDBe 6PGO · UniProt P01116
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