Research workbench
Crystal structure of small molecule beta-lactone 1 covalently bound to K-RAS(G12S)
Analyse Crystal structure of small molecule beta-lactone 1 covalently bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TLE
- Type
- protein
- Length
- 169 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- EC
- 3.6.5.2
- UniProt
- P01116
- Ligands
- I6T, GDP, MG, SO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS (EC 3.6.5.2) | protein | 169 | 36% helix, 25% strand | P01116 |
Ligands and binding sites
- I6T · (3R,4R)-1-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-3-hydroxypiperidine-4-carbaldehyde · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.73 | 0.90 | 23 | I6T |
| 2 | 136 | 0.48 | 0.78 | 27 | MG, GDP |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7TLE · Crystal Structure of small molecule beta-lactone 1 covalently bound to K-Ras(G12S) · 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 7TLE · PDBe 7TLE · UniProt P01116
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