Research workbench
Antibody derived (abd-5) small molecule binding to KRAS.
Analyse Antibody derived (abd-5) small molecule binding to KRAS. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FA2
- Type
- protein
- Length
- 980 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GNP, D2W, MG
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 167 | 37% helix, 26% strand | P01116 |
| B | GTPase KRAS | protein | 168 | 37% helix, 27% strand | P01116 |
| C | GTPase KRAS | protein | 165 | 38% helix, 25% strand | P01116 |
| D | GTPase KRAS | protein | 158 | 37% helix, 26% strand | P01116 |
| E | GTPase KRAS | protein | 164 | 37% helix, 27% strand | P01116 |
| F | GTPase KRAS | protein | 158 | 38% helix, 26% strand | P01116 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- D2W · 4-[2-(dimethylamino)ethoxy]-~{N}-[[(3~{R})-5-(6-methoxypyridin-2-yl)-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]benzamide · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.81 | 0.82 | 141 | empty |
| 2 | 714 | 0.78 | 0.83 | 94 | empty |
| 3 | 177 | 0.61 | 0.83 | 31 | MG, GNP |
| 4 | 231 | 0.58 | 0.79 | 32 | MG, GNP |
| 5 | 175 | 0.55 | 0.80 | 28 | MG, GNP |
Interfaces
12 interfaces between chains.
- B–E · 597 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 586 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 447 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 380 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 375 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6FA2 · Antibody derived (Abd-5) small molecule binding to KRAS. · 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 6FA2 · PDBe 6FA2 · UniProt P01116
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.