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EGFR(T790M/V948R) in complex with LN2057

Analyse EGFR(T790M/V948R) in complex with LN2057 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6V6K
Type: protein
Length: 2,454 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: QQJ, CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, G, H	Epidermal growth factor receptor (EC 2.7.10.1)	protein	314	40% helix, 16% strand	P00533
A	Epidermal growth factor receptor (EC 2.7.10.1)	protein	300	42% helix, 17% strand	P00533
B	Epidermal growth factor receptor (EC 2.7.10.1)	protein	301	43% helix, 16% strand	P00533
C	Epidermal growth factor receptor (EC 2.7.10.1)	protein	302	42% helix, 16% strand	P00533
E	Epidermal growth factor receptor (EC 2.7.10.1)	protein	303	41% helix, 16% strand	P00533
F	Epidermal growth factor receptor (EC 2.7.10.1)	protein	306	42% helix, 17% strand	P00533

Ligands and binding sites

QQJ · N-[3-({4-[4-(4-fluorophenyl)-2-(methylsulfanyl)-1H-imidazol-5-yl]pyridin-2-yl}amino)-4-methoxyphenyl]propanamide · ligand · 8 copies · chains D, A, B, C, E, F, G, H
CL · Chloride ion · ion · 8 copies · chains D, A, B, C, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	638	0.81	0.86	69	QQJ
2	725	0.81	0.84	61	QQJ
3	867	0.80	0.82	78	QQJ
4	914	0.77	0.80	90	QQJ
5	235	0.77	0.90	36	CL, QQJ

Interfaces

14 interfaces between chains.

E–F · 1670 Å² buried · 18 hydrogen bonds · protein-protein
A–H · 1669 Å² buried · 23 hydrogen bonds · protein-protein
C–G · 531 Å² buried · 7 hydrogen bonds · protein-protein
F–H · 464 Å² buried · 7 hydrogen bonds · protein-protein
D–G · 434 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

6V6K · EGFR(T790M/V948R) in complex with LN2057 · 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 B against A, TM-score 0.88

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 6V6K · PDBe 6V6K · UniProt P00533

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