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EGFR kinase (T790M/V948R) in complex with AZ5104

Analyse EGFR kinase (T790M/V948R) in complex with AZ5104 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JXL
Type: protein
Length: 1,163 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: VO7
Pockets: 16 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	Epidermal growth factor receptor (EC 2.7.10.1)	protein	292	45% helix, 17% strand	P00533
A	Epidermal growth factor receptor (EC 2.7.10.1)	protein	294	41% helix, 17% strand	P00533
C	Epidermal growth factor receptor (EC 2.7.10.1)	protein	292	43% helix, 18% strand	P00533
B	Epidermal growth factor receptor (EC 2.7.10.1)	protein	285	44% helix, 18% strand	P00533

Ligands and binding sites

VO7 · N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-5-{[4-(1H-indol-3-yl)pyrimidin-2-yl]amino}-4-methoxyphenyl) propanamide · ligand · 4 copies · chains D, C, A, B

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

Pockets

16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1156	0.81	0.82	87	empty
2	1175	0.80	0.81	100	VO7
3	820	0.70	0.76	61	empty
4	287	0.68	0.83	44	VO7
5	381	0.65	0.79	41	VO7

Interfaces

5 interfaces between chains.

A–B · 644 Å² buried · 7 hydrogen bonds · protein-protein
D–A · 452 Å² buried · 6 hydrogen bonds · protein-protein
D–B · 339 Å² buried · 3 hydrogen bonds · protein-protein
D–C · 214 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 182 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

7JXL · EGFR kinase (T790M/V948R) in complex with AZ5104 · the same entry in another collection · chain B against B, 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 0.90

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 7JXL · PDBe 7JXL · UniProt P00533

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