Fig 1.
EGFR kinase dimers and key structural elements important for catalysis and regulation.
(A) Superposition of A chains of a symmetric dimer (PDB 3GT8, in grey colours) and an asymmetric dimer (PDB 3IKA, in blue colours). Interfaces are depicted with dotted lines. (B) Active monomeric conformer with an ATP analog+peptide conjugate (PDB 2GS6). Key structural elements are coloured magenta (Gly-rich loop), blue (αC helix), violet (activation segment), green (catalytic loop), and sites in red (K745 in the AxK motif), orange (T790 gatekeeper), yellow (catalytic spine residues) and cyan (regulatory spine residues). Ion pair (salt-bridge) between K745 and E762 is depicted with a dashed green line. (C) Comparison of these elements in active (PDB 2GS6) and inactive (PDB 3W32) monomers following the same colour scheme, but in lighter tones. Main transitions of these elements from active to inactive are depicted with black arrows.
Fig 2.
Positions belonging to and in close contact with the main pocket.
Exon: shows the limits of each exon. Region: informs the conserved regions involved in catalytic control. Abbreviations: CS: catalytic spine; ADi, SDi: assymetric/symmetric dimer interface; RS: regulatory spine; GK: gatekeeper. Position, list number and residue for each position in the main pocket and close contact. P/C: depicts whether a position is considered as part of the main pocket (P) or in close contact (C). Position and P/C rows are coloured, according to the considerations in P/C, for those sites with defined coordinates in all the structures used in the present work. Those in white correspond to positions that are found as missing in at least one of these structures.
Fig 3.
Main pocket comparison between active (left, PDB 2GS6 with ATP analog–peptide conjugate) and inactive (right, PDB 3W32 with pyrimido [4,5-b]azepine-derived inhibitor) monomers, following the same colouring scheme as in Figs 1 and 2 (active: A colours, inactive: I colours). The 53 main pocket positions are represented as surfaces in both monomers. For the symmetric and asymmetric interface residues, only those included or in close contact to the main pocket are depicted in black and bright green, respectively.
Fig 4.
Hierarchical clustering based on the α-carbon RMSD, using only main pocket residues. Node A divides active and inactive conformations. Node B includes a particular group (PDBids: 5HG5:A; 5HG7:A; 5HG8:A) as part of active conformations’ group (see EGFR main pocket definition, alignment and clustering section in Results).
Fig 5.
Variant site mapping over kinase domain conformers.
The main pocket is represented as a surface. From left to right and from top to bottom: active monomer with ATP analog–peptide conjugate (PDB id 2GS6), inactive monomer with pyrimido[4,5-b]azepine-derived inhibitor (PDB id 3W32), active chain in asymmetric dimer with WZ4002 irreversible inhibitor (PDB id 3IKA_A), and inactive chain in asymmetric dimer (PDB id 3IKA_B). The most frequently affected sites (those in red, violet and dark blue) map in the catalytic pocket and are found in particular regions: the activation segment (with the classical L858R), the Gly-rich loop, and the region that connects both lobes of the kinase. Interestingly, most of the residues that serve as the docking site for the substrate peptide are not affected by variations (circled with a dashed black line). The total number of missense substitutions observed in COSMIC for each position is listed in S2 Table, column Gen_var_count_ocurrence. Missing regions are connected with straight dashed lines.