Table 1.
DFG-in structures of protein kinases for DFG-out conformation prediction.
Figure 1.
Analyses of kinase DFG-out structures.
(A) Superposition of the DFG-in and DFG-out structures of LCK (PDB codes: 3LCK and 2PL0, respectively), and the conserved residues that characterize the space of the active-site cleft (LCK numbering: K273, E288, D382, and F383). (B) Rotation axis of the N-lobe shown by the LCK DFG-in structure. (C) Superposition of the LCK DFG-out structure and the DFG-in structure with the rotated N-lobe. (D) Analyses of the active-site cleft of the kinase ABL1 DFG-out structure (PDB code: 2F4J) using the programs PASS and LIGSITE. The three red spheres B1, B2, and B3 represent the three binding site centers identified by PASS. The grid points enclosed with the gray mesh represent the cleft binding pocket identified by LIGSITE.
Table 2.
Three categories of the N-lobe rotations in the DFG-in structures.
Table 3.
Numbers of occupied water molecules in the active-site clefts of kinase DFG-out structures in complex with type-II inhibitors.
Figure 2.
The activation-loop remodeling method (ALRM) and the vitual molecule defined for selecting the DFG-out models.
(A) Flowchart of the ALRM approach. (B) The structure of the virtual molecule that resembles the minimum core scaffold of typical type-II inhibitors.
Table 4.
The percentages of DFG-out models, populations of major activation-loop clusters, TM-score values and heavy-atom RMSDs of DFG-motif with respect to the corresponding crystal structures.
Figure 3.
Representative DFG-out models of the major activation-loop clusters.
(A) ABL1. (B) BRAF1. (C) EPHA3. (D) KIT. (E) LCK. (F) MK14. (G) SRC.
Figure 4.
Superposition of DFG motifs in the DFG-out models with respect to those in the crystal structures.
(A) ABL1. (B) BRAF1. (C) EPHA3. (D) KIT. (E) LCK. (F) MK14. (G) SRC.
Table 5.
RMSDs of the lowest-energy representative poses of type-II inhibitors with respect to those in the crystal structures using DFG-out models and crystal structures, respectively.
Figure 5.
Superposition of the predicted binding poses of type-II ligands with respect to those in crystal structures for 24 known kinase-inhibitor pairs.
Figure 6.
Docking pose with a relatively large RMSD and correlation of docking energies.
(A) Steric clash in the DFG-out models of LCK. (B) Correlation of the docking energies based on the DFG-out models with those based on the crystal structures.
Figure 7.
Performance of virtual screening for type-II inhibitors using the predicted DFG-out models, as shown by the AUC (area under curve) values.
(A) ABL1. (B) BRAF1. (C) EPHA3. (D) KIT. (E) LCK. (F) MK14. (G) SRC.
Figure 8.
Vectors defined for conformational classification of predicted kinase models.
(A) Topview of the aligned DFG-in and DFG-out structures. (B) Vector definitions in the DFG-in structures. (C) Vector definitions in the DFG-out structures.