MolNFT v1 · #81984 · protein
Crystal structure of interleukin-2 inducible T-cell kinase itk catalytic domain with thienopyrazolylindole inhibitor 477
3V8T · Tyrosine-protein kinase ITK/TSK: “Crystal structure of interleukin-2 inducible T-cell kinase itk catalytic domain with thienopyrazolylindole…”. X-ray diffraction, 2 ligands (477, SO4), 6 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 3V8T
- Type
- protein
- Length
- 482 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
- 477, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 238 | 42% helix, 17% strand | Q08881 |
| B | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 244 | 45% helix, 17% strand | Q08881 |
Ligands and binding sites
- 477 · 3-{2-[5-(difluoromethyl)-2H-thieno[3,2-c]pyrazol-3-yl]-1H-indol-6-yl}pentan-3-ol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.76 | 0.81 | 52 | empty |
| 2 | 190 | 0.57 | 0.80 | 24 | 477 |
| 3 | 182 | 0.57 | 0.80 | 25 | 477 |
| 4 | 54 | 0.49 | 0.86 | 14 | empty |
| 5 | 55 | 0.46 | 0.84 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1325 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 3V8T · Crystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Catalytic Domain with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q08881 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ITK/TSK (Q08881) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 3V8T · PDBe 3V8T · UniProt Q08881
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