MolNFT v1 · #99156 · protein
Crystal structure of small molecule disulfide 4 covalently bound to K- RAS G12C
4LV6 · GTPase KRAS: “Crystal structure of small molecule disulfide 4 covalently bound to K- RAS G12C”. X-ray diffraction, 3 ligands (20H, GDP, CA), 4 pockets (best druggability 0.67). MolNFT v1 #99156 on GenesisL1: 3D structure, binding…
- PDB
- 4LV6
- Type
- protein
- Length
- 335 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- 20H, GDP, CA
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 37% 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 | 167 | 37% helix, 26% strand | P01116 |
Ligands and binding sites
- 20H · 1-[(2,4-dichlorophenoxy)acetyl]-N-(2-sulfanylethyl)piperidine-4-carboxamide · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.67 | 0.80 | 49 | CA, 20H, GDP |
| 2 | 383 | 0.66 | 0.80 | 50 | CA, 20H, GDP |
| 3 | 127 | 0.53 | 0.81 | 20 | empty |
| 4 | 137 | 0.48 | 0.78 | 29 | CA |
Interfaces
1 interface between chains.
- A–B · 509 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4LV6 · Crystal Structure of small molecule disulfide 4 covalently bound to K-Ras G12C · 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 4LV6 · PDBe 4LV6 · UniProt P01116
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