Research workbench
ERBB4 kinase domain complexed with a thienopyrimidine inhibitor
Analyse ERBB4 kinase domain complexed with a thienopyrimidine inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R4B
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-4
- EC
- 2.7.10.1
- UniProt
- Q15303
- Ligands
- GW7
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor tyrosine-protein kinase erbb-4 (EC 2.7.10.1) | protein | 292 | 38% helix, 16% strand | Q15303 |
| B | Receptor tyrosine-protein kinase erbb-4 (EC 2.7.10.1) | protein | 291 | 38% helix, 16% strand | Q15303 |
Ligands and binding sites
- GW7 · N-{3-chloro-4-[(3-fluorobenzyl)oxy]phenyl}-6-ethylthieno[3,2-d]pyrimidin-4-amine · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.73 | 0.85 | 42 | GW7 |
| 2 | 275 | 0.72 | 0.86 | 32 | GW7 |
| 3 | 295 | 0.56 | 0.76 | 36 | empty |
| 4 | 146 | 0.41 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 335 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2R4B · ErbB4 kinase domain complexed with a thienopyrimidine inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q15303 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-4 (Q15303) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 Q15303
- Elsewhere: RCSB PDB 2R4B · PDBe 2R4B · UniProt Q15303
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