Research workbench
Aurora B kinase in complex with vx-680
Analyse Aurora B kinase in complex with vx-680 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B8M
- Type
- protein
- Length
- 635 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aurora kinase B-a; Inner centromere protein a
- EC
- 2.7.11.1
- UniProt
- Q6DE08, O13024
- Ligands
- VX6
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aurora kinase B-a (EC 2.7.11.1) | protein | 271 | 39% helix, 18% strand | Q6DE08 |
| B | Aurora kinase B-a (EC 2.7.11.1) | protein | 280 | 38% helix, 18% strand | Q6DE08 |
| C | Inner centromere protein a | protein | 41 | 63% helix, 2% strand | O13024 |
| D | Inner centromere protein a | protein | 43 | 53% helix, 0% strand | O13024 |
Ligands and binding sites
- VX6 · Cyclopropanecarboxylic acid {4-[4-(4-methyl-piperazin-1-yl)-6-(5-methyl-2H-pyrazol-3-ylamino)-pyrimidin-2-ylsulfanyl]-phenyl}-amide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.75 | 0.87 | 28 | empty |
| 2 | 303 | 0.72 | 0.85 | 29 | empty |
| 3 | 406 | 0.72 | 0.83 | 46 | VX6 |
| 4 | 463 | 0.67 | 0.79 | 42 | VX6 |
| 5 | 61 | 0.33 | 0.76 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–D · 1856 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1849 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4B8M · Aurora B kinase in complex with VX-680 · the same entry in another collection · chain D against D, TM-score 1.00
- Q6DE08 · AlphaFold monomer V2.0 prediction for aurora kinase B-a (Q6DE08) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O13024 · AlphaFold monomer V2.0 prediction for inner centromere protein a (O13024) · a predicted model of the same protein · chain C against A, TM-score 0.61
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 Q6DE08
- Every structure of UniProt O13024
- Elsewhere: RCSB PDB 4B8M · PDBe 4B8M · UniProt Q6DE08 · UniProt O13024
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