MolNFT v1 · #191269 · protein
Crystal structure of small molecule ALPHA,BETA-ketoamide 4 covalently bound to K-RAS(G12R)
8CX5 · Isoform 2B of GTPase KRAS: “Crystal structure of small molecule ALPHA,BETA-ketoamide 4 covalently bound to K-RAS(G12R)”. X-ray diffraction, 5 ligands (P7U, GDP, MG), 3 pockets (best druggability 0.71). MolNFT v1 #191269 on…
- PDB
- 8CX5
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2B of GTPase KRAS
- EC
- 3.6.5.2
- Ligands
- P7U, GDP, MG, NA, PO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 170 | 36% helix, 26% strand | — |
Ligands and binding sites
- P7U · {(2S)-4-[(7P)-7-(8-chloronaphthalen-1-yl)-8-fluoro-2-{[(4R,7as)-tetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]-1-[(3S)-2,2,3-trihydroxybutanoyl]piperazin-2-yl}acetonitrile · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- PO4 · Phosphate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.71 | 0.84 | 45 | MG, P7U, GDP |
| 2 | 315 | 0.71 | 0.84 | 42 | MG, P7U, GDP |
| 3 | 246 | 0.63 | 0.82 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 438 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 8CX5 · Crystal Structure of small molecule alpha,beta-ketoamide 4 covalently bound to K-Ras(G12R) · 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
- Elsewhere: RCSB PDB 8CX5 · PDBe 8CX5
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