Kinase Conformation Resource
A web resource for protein kinase sequence, structure and phylogeny.
Protein kinases (PKs) are enzymes that transfer phosphoryl group from an ATP molecule to Ser, Thr or Tyr residue of the substrate protein. The human genome consists 484 PK genes (497 domains) that are divided broadly into nine families based on their sequences namely, AGC, CAMK, CK1, CMGC, NEK, RGC, STE, TKL, TYR and OTHER (unclassified). They share a conserved structural fold consisting of two lobes: an N-terminal lobe, formed by five stranded β-sheet with an α-helix called the C-helix, and a C-terminal lobe comprising six α-helices. The two lobes are connected by a flexible region in the middle which forms the ATP binding active site of the protein.
The activation loop is typically 20-30 residues in length and is the most critical secondary structural element of the active site of PKs. It is in completely extended conformation in the catalytically active state of the enzyme facilitating the binding of ATP molecule and the substrate. However, it folds on the surface of the protein in different kinds of inactive states. The activation loop begins with a conserved sequence motif called DFGmotif (Asp, Phe, and Gly residues). These residues are observed to be in a unique orientation when the loop is extended (active state) but display remarkable flexibility in folded (inactive) loop conformations.
Typical structure of protein kinase
Multiple orientations of DFG-Phe in EGFR
We have determined the location of DFG-Phe ring in the binding pocket based on its distance from two
Based on the spatial location of DFG-Phe ring in the binding pocket we have classified kinase structures into three broad groups:
Each spatial group consists of multiple closely related conformations. To cluster these conformations we used the backbone dihedrals (φ,ψ) of X-DFG (residue before conserved Asp), DFG-Asp, DFG-Phe and side chain dihedral (χ1) of DFG-Phe. These dihedrals we used to compute a distance matrix which is then provided as an input to DBSCAN (Density-based spatial clustering of applications with noise), a density-based clustering algorithm. The different clusters observed are labeled on the basis of Ramachandran region (A, B, L, and E) occupied by XDF residue backbone and the DFG-Phe χ1 rotamer (minus = -60°; plus = +60°; trans = 180°).
For the DFGin group we obtained six clusters labeled as BLAminus, BLAplus, ABAminus, BLBminus, BLBplus, and BLBtrans. All the catalytically primed structures (ATP+Mg bound and activation loop phosphorylated) are observed in the BLAminus cluster.
For the DFGout group we obtained just one cluster. In this cluster, the X-D-F residues occupy the B-B-A regions of the Ramachandran map and DFG-Phe is in a -60° rotamer. More than 82% of Type 2 inhibitor bound structures are BBAminus; the remainder are in the DFGout noise group.
The structures in the DFGinter conformation display more variability than the other states. For the DFGinter group we obtained only one small cluster. The X-D-F residues are in a B-A-B conformation and the DFG-Phe residue is observed in a trans rotamer with a few chains displaying a rotamer orientation between g-minus and trans.
We have classified PK inhibitors into five groups based on the region of protein they bind to.
A list of FDA approved PK inhibitors with known structures can be accessed here.