Research workbench
Crystal structure of the PCTAIRE1 kinase in complex with inhibitor
Analyse Crystal structure of the PCTAIRE1 kinase in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G6V
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 16
- EC
- 2.7.11.22
- UniProt
- Q00536
- Ligands
- 919
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 16 (EC 2.7.11.22) | protein | 308 | 37% helix, 16% strand | Q00536 |
| B | Cyclin-dependent kinase 16 (EC 2.7.11.22) | protein | 302 | 39% helix, 16% strand | Q00536 |
Ligands and binding sites
- 919 · 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.85 | 0.86 | 98 | 919 |
| 2 | 144 | 0.60 | 0.84 | 27 | empty |
| 3 | 79 | 0.41 | 0.79 | 15 | EDO |
| 4 | 74 | 0.35 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1736 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5G6V · Crystal structure of the PCTAIRE1 kinase in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q00536 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 16 (Q00536) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q00536
- Elsewhere: RCSB PDB 5G6V · PDBe 5G6V · UniProt Q00536
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