Research workbench
KRASG12C in complex with GDP and compound 3
Analyse KRASG12C in complex with GDP and compound 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R0Q
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- H0O, GDP, MG
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 168 | 38% helix, 26% strand | P01116 |
| B | GTPase KRAS | protein | 166 | 38% helix, 26% strand | P01116 |
Ligands and binding sites
- H0O · ~{N}-[4-[3,5-dimethyl-4-(5-methyl-2~{H}-indazol-4-yl) pyrazol-1-yl]phenyl]propanamide · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.71 | 0.83 | 44 | MG, H0O, GDP |
| 2 | 375 | 0.71 | 0.83 | 46 | MG, H0O, GDP |
| 3 | 177 | 0.59 | 0.82 | 26 | empty |
| 4 | 138 | 0.50 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 514 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7R0Q · KRasG12C in complex with GDP and compound 3 · 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 7R0Q · PDBe 7R0Q · UniProt P01116
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