Research workbench
KRAS G12C in bound to quinazoline based switch II pocket (swiip) binder
Analyse KRAS G12C in bound to quinazoline based switch II pocket (swiip) binder in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V71
- Type
- protein
- Length
- 1,014 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GDP, 8ZG, MG
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | GTPase KRAS | protein | 169 | 37% helix, 25% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- 8ZG · 1-{4-[6-chloro-7-(2-fluorophenyl)quinazolin-4-yl]piperazin-1-yl}propan-1-one · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.66 | 0.78 | 57 | GDP, MG, 8ZG |
| 2 | 521 | 0.64 | 0.76 | 42 | empty |
| 3 | 294 | 0.62 | 0.79 | 48 | GDP, MG, 8ZG |
| 4 | 286 | 0.61 | 0.79 | 41 | GDP, MG, 8ZG |
| 5 | 235 | 0.55 | 0.78 | 39 | GDP, MG, 8ZG |
Interfaces
9 interfaces between chains.
- C–D · 524 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 400 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 324 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 240 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 129 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 5V71 · 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 5V71 · PDBe 5V71 · UniProt P01116
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