Research workbench
Discovery of small molecules binding to KRAS via high affinity antibody fragment competition method.
Analyse Discovery of small molecules binding to KRAS via high affinity antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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