PDBsum entry 5d11

Transferase

PDB id: 5d11

Contents

Protein chains

254 a.a.

Ligands

GOL ×2

56G ×2

Waters ×98

PDB id:

5d11

Name:

Transferase

Title:

Kinase domain of csrc in complex with rl235

Structure:

Proto-oncogene tyrosine-protein kinase src. Chain: a, b. Synonym: proto-oncogenE C-src,pp60c-src,p60-src. Engineered: yes. Mutation: yes

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Gene: src. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.30Å R-factor: 0.216 R-free: 0.269

Authors:

C.Becker,C.Gruetter,J.Engel,D.Rauh

Key ref:

J.Engel et al. (2015). Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach. J Med Chem, 58, 6844-6863. PubMed id: 26275028 DOI: 10.1021/acs.jmedchem.5b01082

Date:

03-Aug-15 Release date: 09-Sep-15

Protein chains

P00523  (SRC_CHICK) -  Proto-oncogene tyrosine-protein kinase Src from Gallus gallus

Seq: 533 a.a.

Struc: 254 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.10.2 - non-specific protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/acs.jmedchem.5b01082

J Med Chem 58:6844-6863 (2015)

PubMed id: 26275028

Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach.

J.Engel, A.Richters, M.Getlik, S.Tomassi, M.Keul, M.Termathe, J.Lategahn, C.Becker, S.Mayer-Wrangowski, C.Grütter, N.Uhlenbrock, J.Krüll, N.Schaumann, S.Eppmann, P.Kibies, F.Hoffgaard, J.Heil, S.Menninger, S.Ortiz-Cuaran, J.M.Heuckmann, V.Tinnefeld, R.P.Zahedi, M.L.Sos, C.Schultz-Fademrecht, R.K.Thomas, S.M.Kast, D.Rauh.

ABSTRACT

Receptor tyrosine kinases represent one of the prime targets in cancer therapy, as the dysregulation of these elementary transducers of extracellular signals, like the epidermal growth factor receptor (EGFR), contributes to the onset of cancer, such as non-small cell lung cancer (NSCLC). Strong efforts were directed to the development of irreversible inhibitors and led to compound CO-1686, which takes advantage of increased residence time at EGFR by alkylating Cys797 and thereby preventing toxic effects. Here, we present a structure-based approach, rationalized by subsequent computational analysis of conformational ligand ensembles in solution, to design novel and irreversible EGFR inhibitors based on a screening hit that was identified in a phenotype screen of 80 NSCLC cell lines against approximately 1500 compounds. Using protein X-ray crystallography, we deciphered the binding mode in engineered cSrc (T338M/S345C), a validated model system for EGFR-T790M, which constituted the basis for further rational design approaches. Chemical synthesis led to further compound collections that revealed increased biochemical potency and, in part, selectivity toward mutated (L858R and L858R/T790M) vs nonmutated EGFR. Further cell-based and kinetic studies were performed to substantiate our initial findings. Utilizing proteolytic digestion and nano-LC-MS/MS analysis, we confirmed the alkylation of Cys797.