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EGFR(T790M/V948R) in complex with LN3844

Analyse EGFR(T790M/V948R) in complex with LN3844 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WXN
Type: protein
Length: 1,179 residues
Chains: 4
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: UEJ, ANP, MG, CL
Pockets: 18 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	Epidermal growth factor receptor (EC 2.7.10.1)	protein	292	43% helix, 16% strand	P00533
A	Epidermal growth factor receptor (EC 2.7.10.1)	protein	298	42% helix, 17% strand	P00533
B	Epidermal growth factor receptor (EC 2.7.10.1)	protein	303	41% helix, 17% strand	P00533
C	Epidermal growth factor receptor (EC 2.7.10.1)	protein	286	44% helix, 14% strand	P00533

Ligands and binding sites

UEJ · N-(3-{5-[2-(acetylamino)pyridin-4-yl]-2-(methylsulfanyl)-1H-imidazol-4-yl}phenyl)-2-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-6-fluoro-3-hydroxybenzamide · ligand · 2 copies · chains D, C
ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains B
MG · Magnesium ion · metal · chains B
CL · Chloride ion · ion · chains C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	923	0.85	0.86	88	UEJ
2	306	0.80	0.90	25	empty
3	567	0.79	0.85	77	ANP, MG
4	470	0.77	0.85	62	UEJ
5	434	0.74	0.83	48	empty

Interfaces

6 interfaces between chains.

B–C · 1922 Å² buried · 27 hydrogen bonds · protein-protein
D–A · 1628 Å² buried · 16 hydrogen bonds · protein-protein
D–B · 571 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 430 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 46 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6WXN · EGFR(T790M/V948R) in complex with LN3844 · the same entry in another collection · chain C against C, TM-score 1.00
P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain B against A, TM-score 0.89

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 6WXN · PDBe 6WXN · UniProt P00533

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