Research workbench
Crystal structure of EGFR T790M/V948R in complex with covalent pyrrolopyrimidine 18D
Analyse Crystal structure of EGFR T790M/V948R in complex with covalent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TFW
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- 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
- N7W, MG, SO4, CL
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 266 | 43% helix, 19% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 264 | 44% helix, 19% strand | P00533 |
Ligands and binding sites
- N7W · ~{N}-[5-[4-[[3-chloranyl-4-(pyridin-2-ylmethoxy) phenyl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]-2-[2-(dimethylamino)ethoxy]phenyl]propanamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.80 | 0.86 | 76 | SO4 |
| 2 | 551 | 0.71 | 0.80 | 58 | N7W, MG, CL |
| 3 | 295 | 0.64 | 0.80 | 39 | SO4, N7W, MG |
| 4 | 81 | 0.36 | 0.76 | 16 | empty |
| 5 | 99 | 0.33 | 0.72 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1256 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6TFW · Crystal Structure of EGFR T790M/V948R in Complex with Covalent Pyrrolopyrimidine 18d · the same entry in another collection · chain A against A, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 6TFW · PDBe 6TFW · UniProt P00533
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