MolNFT v1 · #136968 · protein
KRAS G12C in bound to quinazoline based switch II pocket (swiip) binder
5V9L · GTPase KRAS: “KRAS G12C in bound to quinazoline based switch II pocket (swiip) binder”. X-ray diffraction, 3 ligands (GDP, 91D, MG), 5 pockets (best druggability 0.55). MolNFT v1 #136968 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5V9L
- Type
- protein
- Length
- 507 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GDP, 91D, MG
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | GTPase KRAS | protein | 169 | 37% helix, 25% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- 91D · N~3~-[6-chloro-7-(2-fluorophenyl)-4-(4-propanoylpiperazin-1-yl)quinazolin-2-yl]-N,N-dimethyl-beta-alaninamide · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
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 | 239 | 0.55 | 0.78 | 40 | GDP, MG, 91D |
| 2 | 286 | 0.54 | 0.75 | 36 | empty |
| 3 | 207 | 0.53 | 0.77 | 38 | GDP, MG, 91D |
| 4 | 202 | 0.52 | 0.77 | 40 | GDP, MG, 91D |
| 5 | 78 | 0.31 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 413 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 5V9L · KRAS G12C in bound to quinazoline based switch II pocket (SWIIP) binder · 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 5V9L · PDBe 5V9L · UniProt P01116
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