MolNFT v1 · #125092 · protein
Covalent GTP-competitive inhibitors of KRAS G12C: guanosine bisphosphonate analogs
5KYK · GTPase KRAS: “Covalent GTP-competitive inhibitors of KRAS G12C: guanosine bisphosphonate analogs”. X-ray diffraction, 1 ligand (6ZD), 7 pockets (best druggability 0.79). MolNFT v1 #125092 on GenesisL1: 3D structure, binding sites…
- PDB
- 5KYK
- Type
- protein
- Length
- 483 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- 6ZD
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 159 | 37% helix, 26% strand | P01116 |
| B | GTPase KRAS | protein | 160 | 36% helix, 26% strand | P01116 |
| C | GTPase KRAS | protein | 164 | 35% helix, 25% strand | P01116 |
Ligands and binding sites
- 6ZD · 5'-O-[(R)-[({2-[(chloroacetyl)amino]ethyl}sulfamoyl) methyl](hydroxy)phosphoryl]guanosine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.79 | 0.81 | 112 | empty |
| 2 | 133 | 0.51 | 0.80 | 19 | empty |
| 3 | 126 | 0.47 | 0.78 | 18 | empty |
| 4 | 218 | 0.47 | 0.74 | 25 | empty |
| 5 | 110 | 0.41 | 0.77 | 26 | 6ZD |
Interfaces
3 interfaces between chains.
- A–B · 344 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 331 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 330 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 covalent (covalent ligand).
Compared structures
- 5KYK · Covalent GTP-competitive inhibitors of KRAS G12C: Guanosine bisphosphonate Analogs · 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 5KYK · PDBe 5KYK · UniProt P01116
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