MolNFT v1 · #52135 · protein
Structure of aurora B kinase in complex with ZM447439
2VRX · SERINE/THREONINE-protein kinase 12-a: “Structure of aurora B kinase in complex with ZM447439”. X-ray diffraction, 1 ligand (447), 6 pockets (best druggability 0.76). MolNFT v1 #52135 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VRX
- Type
- protein
- Length
- 627 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
- 447
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase 12-a (EC 2.7.11.1) | protein | 269 | 40% helix, 19% strand | Q6DE08 |
| B | SERINE/THREONINE-protein kinase 12-a (EC 2.7.11.1) | protein | 275 | 38% helix, 18% strand | Q6DE08 |
| C | Inner centromere protein a | protein | 40 | 60% helix, 0% strand | O13024 |
| D | Inner centromere protein a | protein | 43 | 53% helix, 0% strand | O13024 |
Ligands and binding sites
- 447 · N-(4-{[6-methoxy-7-(3-morpholin-4-ylpropoxy)quinazolin-4-yl]amino}phenyl)benzamide · 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 | 294 | 0.76 | 0.88 | 28 | empty |
| 2 | 279 | 0.73 | 0.86 | 29 | empty |
| 3 | 412 | 0.64 | 0.78 | 40 | 447 |
| 4 | 280 | 0.57 | 0.77 | 38 | 447 |
| 5 | 57 | 0.33 | 0.77 | 13 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1803 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1800 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2VRX · Structure of Aurora B kinase in complex with ZM447439 · 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 0.60
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 2VRX · PDBe 2VRX · UniProt Q6DE08 · UniProt O13024
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