Research workbench
KRASG12C GDP form in complex with CPD4
Analyse KRASG12C GDP form in complex with CPD4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A47
- Type
- protein
- Length
- 501 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2B of GTPase KRAS
- EC
- 3.6.5.2
- Ligands
- GDP, QY5
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 167 | 37% helix, 23% strand | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, C, E
- QY5 · ~{N}-[3-bromanyl-2-(2-methylimidazol-1-yl)pyridin-4-yl]-3-[[3-bromanyl-2-(2-methylimidazol-1-yl)pyridin-4-yl]-propanoyl-amino]propanamide · ligand · 3 copies · chains A, C, E
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 | 268 | 0.58 | 0.78 | 36 | GDP, QY5 |
| 2 | 288 | 0.57 | 0.77 | 27 | empty |
| 3 | 279 | 0.56 | 0.77 | 44 | GDP, QY5 |
| 4 | 220 | 0.55 | 0.78 | 34 | GDP, QY5 |
| 5 | 94 | 0.39 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- C–E · 543 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7A47 · KRASG12C GDP form in complex with Cpd4 · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 7A47 · PDBe 7A47
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.