Research workbench
Quinolin-6-yloxyacetamides are microtubule destabilizing agents that bind to the colchicine site of tubulin
Analyse Quinolin-6-yloxyacetamides are microtubule destabilizing agents that bind to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O7A
- Type
- protein
- Length
- 2,089 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Uncharacterized protein
- UniProt
- P81947, Q6B856, P63043, E1BQ43
- Ligands
- GTP, GDP, 9N5, ACP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 46% helix, 19% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 421 | 48% helix, 20% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 419 | 50% helix, 18% strand | Q6B856 |
| E | Stathmin-4 | protein | 118 | 80% helix, 13% strand | P63043 |
| F | Uncharacterized protein | protein | 254 | 31% helix, 20% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
- 9N5 · (2~{R})-2-(3-ethynylquinolin-6-yl)oxy-2-methoxy-~{N}-[(1~{E})-1-methoxyimino-2-methyl-propan-2-yl]ethanamide · ligand · 2 copies · chains B, D
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.85 | 0.86 | 136 | GTP, MG, 9N5 |
| 2 | 868 | 0.84 | 0.86 | 103 | GTP, MG, 9N5 |
| 3 | 829 | 0.81 | 0.84 | 100 | GDP, MG |
| 4 | 188 | 0.79 | 0.94 | 37 | empty |
| 5 | 382 | 0.72 | 0.83 | 40 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1500 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1428 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1360 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 926 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 851 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5O7A · Quinolin-6-yloxyacetamides are microtubule destabilizing agents that bind to the… · 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 P81947
- Every structure of UniProt Q6B856
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 5O7A · PDBe 5O7A · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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