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Crystal structure of interleukin-2 inducible T-cell kinase itk catalytic domain with thienopyrazolylindole inhibitor 090
Analyse Crystal structure of interleukin-2 inducible T-cell kinase itk catalytic domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V5J
- 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
- 0F2, SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 241 | 42% helix, 17% strand | Q08881 |
| B | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 241 | 42% helix, 17% strand | Q08881 |
Ligands and binding sites
- 0F2 · 3-[4-(2-morpholin-4-ylethoxy)-2-(1~{H}-thieno[3,2-c]pyrazol-3-yl)-1~{H}-indol-6-yl]pentan-3-ol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 663 | 0.75 | 0.80 | 52 | empty |
| 2 | 205 | 0.58 | 0.80 | 24 | 0F2 |
| 3 | 169 | 0.54 | 0.79 | 21 | 0F2 |
| 4 | 50 | 0.48 | 0.86 | 15 | empty |
| 5 | 51 | 0.45 | 0.85 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1332 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 3V5J · 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 0.97
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 3V5J · PDBe 3V5J · UniProt Q08881
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