MolNFT v1 · #103731 · protein
Itk kinase domain with compound 27 (N-{1-[(1R)-3-(dimethylamino)-1- phenylpropyl]-1H-pyrazol-4-yl}-6-(1H-pyrazol-4-yl)-1H-indazole-3- carboxamide)
4PPC · Tyrosine-protein kinase ITK/TSK: “Itk kinase domain with compound 27 (N-{1-[(1R)-3-(dimethylamino)-1…”. X-ray diffraction, 1 ligand (2VW), 3 pockets (best druggability 0.73). MolNFT v1 #103731 on GenesisL1: 3D structure, binding…
- PDB
- 4PPC
- Type
- protein
- Length
- 464 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
- 2VW
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 233 | 42% helix, 19% strand | Q08881 |
| B | Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) | protein | 231 | 44% helix, 19% strand | Q08881 |
Ligands and binding sites
- 2VW · N-{1-[(1R)-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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.73 | 0.77 | 59 | empty |
| 2 | 290 | 0.61 | 0.79 | 40 | 2VW |
| 3 | 240 | 0.60 | 0.79 | 39 | 2VW |
Interfaces
1 interface between chains.
- A–B · 1970 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4PPC · ITK kinase domain with compound 27 (N-{1-[(1R)-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 4PPC · PDBe 4PPC · UniProt Q08881
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