MolNFT v1 · #136894 · protein
KRAS G12C in bound to quinazoline based switch II pocket (swiip) binder
5V71 · GTPase KRAS: “KRAS G12C in bound to quinazoline based switch II pocket (swiip) binder”. X-ray diffraction, 3 ligands (GDP, 8ZG, MG), 11 pockets (best druggability 0.66). MolNFT v1 #136894 on GenesisL1: 3D structure, binding sites…
- 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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