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Crystal structure of interleukin-2 inducible T-cell kinase itk catalytic domain with thienopyrazolylindole inhibitor 542
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
- 3V5L
- Type
- protein
- Length
- 971 residues
- Chains
- 4
- 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
- 0G1, SO4
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 240 | 44% helix, 18% strand | Q08881 |
| B | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 241 | 45% helix, 17% strand | Q08881 |
| C | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 244 | 44% helix, 17% strand | Q08881 |
| D | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 246 | 44% helix, 17% strand | Q08881 |
Ligands and binding sites
- 0G1 · 3-[3-(4-methoxyphenyl)-2-(1H-thieno[3,2-c]pyrazol-3-yl)-1H-indol-6-yl]pentan-3-ol · ligand · 4 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.81 | 0.83 | 73 | 0G1, SO4 |
| 2 | 824 | 0.80 | 0.83 | 64 | 0G1 |
| 3 | 536 | 0.78 | 0.85 | 71 | empty |
| 4 | 140 | 0.67 | 0.88 | 25 | empty |
| 5 | 167 | 0.66 | 0.86 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 777 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 766 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 647 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 600 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3V5L · Crystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Catalytic Domain with… · the same entry in another collection · chain D against D, 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 3V5L · PDBe 3V5L · UniProt Q08881
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