MolNFT v1 · #51750 · protein
Crystal structure of aurora B kinase in complex with reversine inhibitor
2VGO · SERINE/THREONINE-protein kinase 12-a: “Crystal structure of aurora B kinase in complex with reversine inhibitor”. X-ray diffraction, 1 ligand (AD5), 6 pockets (best druggability 0.75). MolNFT v1 #51750 on GenesisL1: 3D structure…
- PDB
- 2VGO
- Type
- protein
- Length
- 631 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase 12-a; Inner centromere protein a
- EC
- 2.7.11.1
- UniProt
- Q6DE08, O13024
- Ligands
- AD5
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase 12-a (EC 2.7.11.1) | protein | 269 | 39% helix, 20% strand | Q6DE08 |
| B | SERINE/THREONINE-protein kinase 12-a (EC 2.7.11.1) | protein | 278 | 37% helix, 19% strand | Q6DE08 |
| C | Inner centromere protein a | protein | 41 | 63% helix, 0% strand | O13024 |
| D | Inner centromere protein a | protein | 43 | 44% helix, 0% strand | O13024 |
Ligands and binding sites
- AD5 · N~6~-cyclohexyl-N~2~-(4-morpholin-4-ylphenyl)-9H-purine-2,6-diamine · 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 | 308 | 0.75 | 0.87 | 27 | empty |
| 2 | 291 | 0.73 | 0.86 | 28 | empty |
| 3 | 271 | 0.64 | 0.81 | 30 | AD5 |
| 4 | 411 | 0.64 | 0.78 | 41 | AD5 |
| 5 | 58 | 0.33 | 0.77 | 13 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1870 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1842 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2VGO · Crystal structure of Aurora B kinase in complex with Reversine inhibitor · 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 2VGO · PDBe 2VGO · UniProt Q6DE08 · UniProt O13024
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