Research workbench
Itk kinase domain with compound 1 (N-[1-(3-cyanobenzyl)-1H-pyrazol-4- yl]-2H-indazole-3-carboxamide)
Analyse Itk kinase domain with compound 1 (N-[1-(3-cyanobenzyl)-1H-pyrazol-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PP9
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase ITK/TSK
- EC
- 2.7.10.2
- UniProt
- Q08881
- Ligands
- 2VT, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 246 | 43% helix, 19% strand | Q08881 |
| B | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 247 | 43% helix, 18% strand | Q08881 |
Ligands and binding sites
- 2VT · N-[1-(3-cyanobenzyl)-1H-pyrazol-4-yl]-2H-indazole-3-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.73 | 0.80 | 69 | empty |
| 2 | 342 | 0.68 | 0.81 | 40 | 2VT |
| 3 | 292 | 0.65 | 0.81 | 38 | 2VT |
Interfaces
1 interface between chains.
- A–B · 1461 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 4PP9 · ITK kinase domain with compound 1 (N-[1-(3-CYANOBENZYL)-1H-PYRAZOL-4-YL]-2H-INDAZOLE-3-CAR… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q08881
- Elsewhere: RCSB PDB 4PP9 · PDBe 4PP9 · UniProt Q08881
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