MolNFT v1 · #118327 · protein
Crystal structure of aurora B in complex with bi 847325
5EYK · Aurora kinase B-a: “Crystal structure of aurora B in complex with bi 847325”. X-ray diffraction, 1 ligand (5U5), 6 pockets (best druggability 0.73). MolNFT v1 #118327 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EYK
- Type
- protein
- Length
- 597 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
- 5U5
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aurora kinase B-a (EC 2.7.11.1) | protein | 264 | 41% helix, 20% strand | Q6DE08 |
| B | Aurora kinase B-a (EC 2.7.11.1) | protein | 276 | 38% helix, 20% strand | Q6DE08 |
| C | Inner centromere protein a | protein | 35 | 57% helix, 0% strand | O13024 |
| D | Inner centromere protein a | protein | 22 | 68% helix, 0% strand | O13024 |
Ligands and binding sites
- 5U5 · 3-[(3~{Z})-3-[[[4-[(dimethylamino)methyl]phenyl]amino]-phenyl-methylidene]-2-oxidanylidene-1~{H}-indol-6-yl]-~{N}-ethyl-prop-2-ynamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.73 | 0.86 | 30 | empty |
| 2 | 314 | 0.73 | 0.85 | 29 | empty |
| 3 | 290 | 0.69 | 0.83 | 32 | 5U5 |
| 4 | 282 | 0.68 | 0.83 | 32 | 5U5 |
| 5 | 62 | 0.34 | 0.77 | 12 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1679 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1000 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5EYK · Crystal structure of aurora B in complex with bi 847325 · 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 D against A, TM-score 0.51
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 5EYK · PDBe 5EYK · UniProt Q6DE08 · UniProt O13024
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