MolNFT v1 · #129183 · protein
Discovery of small molecules binding to KRAS via high affinity antibody fragment competition method.
5OCT · GTPase KRAS: “Discovery of small molecules binding to KRAS via high affinity antibody fragment competition method.”. X-ray diffraction, 3 ligands (9R5, GNP, MG), 11 pockets (best druggability 0.81). MolNFT v1 #129183 on GenesisL1…
- PDB
- 5OCT
- Type
- protein
- Length
- 1,000 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- 9R5, GNP, MG
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 172 | 36% helix, 26% strand | P01116 |
| B | GTPase KRAS | protein | 169 | 37% helix, 26% strand | P01116 |
| C, E, F | GTPase KRAS | protein | 165 | 36% helix, 27% strand | P01116 |
| D | GTPase KRAS | protein | 164 | 37% helix, 27% strand | P01116 |
Ligands and binding sites
- 9R5 · [(2~{R})-6-chloranyl-2,3-dihydro-1,4-benzodioxin-2-yl]methanamine · ligand · 9 copies · chains A, B, C, D, E, F
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.81 | 0.83 | 136 | PEG |
| 2 | 1041 | 0.81 | 0.82 | 122 | empty |
| 3 | 204 | 0.63 | 0.83 | 31 | GNP, MG |
| 4 | 231 | 0.61 | 0.81 | 32 | GNP, MG |
| 5 | 210 | 0.59 | 0.81 | 32 | GNP, MG |
Interfaces
12 interfaces between chains.
- B–E · 828 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 804 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 798 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 376 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 368 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (oxidation).
Compared structures
- 5OCT · Discovery of small molecules binding to KRAS via high affinity antibody fragment… · 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 5OCT · PDBe 5OCT · UniProt P01116
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