Research workbench
Crystal structure of hck in complex with 7-[trans-4-(4- methylpiperazin-1-YL)CYCLOHEXYL]-5-(4-phenoxyphenyl)-7H-PYRROLO[2,3- D]PYRIMIDIN-4-amine (resulting from displacement of SKF86002)
Analyse Crystal structure of hck in complex with 7-[trans-4-(4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LUE
- Type
- protein
- Length
- 841 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase hck
- EC
- 2.7.10.2
- UniProt
- P08631
- Ligands
- VSE, CA, CL
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase hck (EC 2.7.10.2) | protein | 423 | 30% helix, 24% strand | P08631 |
| B | Tyrosine-protein kinase hck (EC 2.7.10.2) | protein | 418 | 29% helix, 24% strand | P08631 |
Ligands and binding sites
- VSE · 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- IMD · Imidazole · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.77 | 0.79 | 74 | empty |
| 2 | 1085 | 0.73 | 0.76 | 102 | IMD |
| 3 | 1159 | 0.73 | 0.76 | 112 | empty |
| 4 | 478 | 0.71 | 0.80 | 47 | VSE, GOL |
| 5 | 528 | 0.71 | 0.80 | 61 | GOL, VSE |
Interfaces
1 interface between chains.
- A–B · 922 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4LUE · Crystal Structure of HCK in complex with 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5… · the same entry in another collection · chain A against A, TM-score 1.00
- P08631 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase hck (P08631) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P08631
- Elsewhere: RCSB PDB 4LUE · PDBe 4LUE · UniProt P08631
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