MolNFT v1 · #184373 · protein
KRASG12C ligand complex
7OO7 · GTPase KRAS: “KRASG12C ligand complex”. X-ray diffraction, 4 ligands (GDP, VLE, MG), 3 pockets (best druggability 0.72). MolNFT v1 #184373 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7OO7
- Type
- protein
- Length
- 336 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- EC
- 3.6.5.2
- UniProt
- P01116
- Ligands
- GDP, VLE, MG, CA
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | GTPase KRAS (EC 3.6.5.2) | protein | 168 | 36% helix, 25% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, D
- VLE · 1-[(6AS)-3-chloro-2-(5-methyl-1H-indazol-4-yl)-5,6,6A, 7,9,10-hexahydro-8H-pyrazino[1',2':5,6][1, 5]oxazocino[4,3,2-de]quinazolin-8-yl]-2-propen-1-one · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
- CA · Calcium ion · metal · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.72 | 0.84 | 41 | MG, GDP, VLE |
| 2 | 369 | 0.69 | 0.81 | 47 | MG, GDP, VLE |
| 3 | 153 | 0.42 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–D · 241 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7OO7 · KRasG12C ligand complex · 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 7OO7 · PDBe 7OO7 · UniProt P01116
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