Research workbench
EGFR kinase domain complexed with an IMIDAZO[2,1-B]THIAZOLE inhibitor
Analyse EGFR kinase domain complexed with an IMIDAZO[2,1-B]THIAZOLE inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LZB
- Type
- protein
- Length
- 1,082 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- ITI
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 265 | 39% helix, 19% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 259 | 39% helix, 19% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 261 | 38% helix, 19% strand | P00533 |
| E, H | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 9 | 78% helix, 0% strand | P00533 |
| F, G | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 7 | 0% helix, 0% strand | P00533 |
Ligands and binding sites
- ITI · N-[3-(5-{2-[(4-morpholin-4-ylphenyl)amino]pyrimidin-4-yl}imidazo[2,1-b][1,3]thiazol-6-yl)phenyl]-2-phenylacetamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.83 | 0.85 | 110 | ITI |
| 2 | 803 | 0.79 | 0.82 | 69 | empty |
| 3 | 606 | 0.78 | 0.84 | 67 | ITI |
| 4 | 548 | 0.72 | 0.80 | 61 | ITI |
| 5 | 359 | 0.71 | 0.83 | 51 | ITI |
Interfaces
9 interfaces between chains.
- A–B · 574 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 368 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 366 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 323 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 246 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3LZB · EGFR kinase domain complexed with an imidazo[2,1-b]thiazole inhibitor · the same entry in another collection · chain H against H, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 P00533
- Elsewhere: RCSB PDB 3LZB · PDBe 3LZB · UniProt P00533
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