Research workbench
Itk kinase domain with compound 28 (N-{1-[(1S)-3-(dimethylamino)-1- phenylpropyl]-1H-pyrazol-4-yl}-6-(1H-pyrazol-4-yl)-1H-indazole-3- carboxamide)
Analyse Itk kinase domain with compound 28 (N-{1-[(1S)-3-(dimethylamino)-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PPB
- Type
- protein
- Length
- 478 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
- 2VV
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 239 | 45% helix, 20% strand | Q08881 |
Ligands and binding sites
- 2VV · N-{1-[(1S)-3-(dimethylamino)-1-phenylpropyl]-1H-pyrazol-4-yl}-6-(1H-pyrazol-4-yl)-1H-indazole-3-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.72 | 0.80 | 49 | 2VV |
| 2 | 411 | 0.67 | 0.80 | 45 | 2VV |
| 3 | 51 | 0.37 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1819 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4PPB · ITK kinase domain with compound 28 (N-{1-[(1S)-3-(DIMETHYLAMINO)-1-PHENYLPROPYL]-1H-PYRAZO… · 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 4PPB · PDBe 4PPB · UniProt Q08881
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