MolNFT v1 · #164994 · protein
Crystal structure of EGFR T790M/V948R in complex with covalent pyrrolopyrimidine 18C
6TFY · Epidermal growth factor receptor: “Crystal structure of EGFR T790M/V948R in complex with covalent pyrrolopyrimidine 18C”. X-ray diffraction, 2 ligands (N7Z, SO4), 5 pockets (best druggability 0.72). MolNFT v1 #164994 on GenesisL1…
- PDB
- 6TFY
- 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
- N7Z, SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% 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
- N7Z · ~{N}-[5-[4-[[3-chloranyl-4-(pyridin-2-ylmethoxy) phenyl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]-2-(3-oxidanylpropoxy)phenyl]propanamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.72 | 0.80 | 67 | N7Z |
| 2 | 505 | 0.71 | 0.81 | 76 | SO4 |
| 3 | 442 | 0.69 | 0.80 | 51 | N7Z |
| 4 | 94 | 0.37 | 0.75 | 18 | empty |
| 5 | 72 | 0.32 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1366 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6TFY · Crystal Structure of EGFR T790M/V948R in Complex with Covalent Pyrrolopyrimidine 18c · 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 6TFY · PDBe 6TFY · UniProt P00533
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