Research workbench
Itk kinase domain in complex with benzothiazole inhibitor compound 12A (1S,2S)-2-{4-[(DIMETHYLAMINO)METHYL]PHENYL}-N-[6-(pyridin-3-yl)-1,3- benzothiazol-2-YL]CYCLOPROPANECARBOXAMIDE (12A)
Analyse Itk kinase domain in complex with benzothiazole inhibitor compound 12A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MF0
- Type
- protein
- Length
- 477 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
- 29Z
- Pockets
- 4 · best druggability 0.61
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 | 240 | 41% helix, 17% strand | Q08881 |
| B | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 237 | 45% helix, 18% strand | Q08881 |
Ligands and binding sites
- 29Z · (1S,2S)-2-{4-[(dimethylamino)methyl]phenyl}-N-[6-(pyridin-3-yl)-1,3-benzothiazol-2-yl]cyclopropanecarboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.61 | 0.80 | 25 | 29Z |
| 2 | 248 | 0.58 | 0.78 | 33 | 29Z |
| 3 | 100 | 0.48 | 0.80 | 21 | empty |
| 4 | 91 | 0.42 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1854 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4MF0 · ITK kinase domain in complex with benzothiazole inhibitor compound 12a… · 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 0.88
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 4MF0 · PDBe 4MF0 · UniProt Q08881
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