PDBsum entry 1gag

Transferase/transferase inhibitor

PDB id: 1gag

Contents

Protein chains

303 a.a. *

13 a.a. *

Ligands

112

Metals

_MG ×2

Waters ×23

* Residue conservation analysis

PDB id:

1gag

Name:

Transferase/transferase inhibitor

Title:

Crystal structure of the insulin receptor kinase in complex with a bisubstrate inhibitor

Structure:

Insulin receptor, tyrosine kinase domain. Chain: a. Fragment: tyrosine kinase domain. Synonym: ir. Engineered: yes. Mutation: yes. Bisubstrate peptide inhibitor. Chain: b. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.214 R-free: 0.269

Authors:

K.Parang,J.H.Till,A.J.Ablooglu,R.A.Kohanski,S.R.Hubbard,P.A.Cole

Key ref:

K.Parang et al. (2001). Mechanism-based design of a protein kinase inhibitor. Nat Struct Biol, 8, 37-41. PubMed id: 11135668 DOI: 10.1038/83028

Date:

29-Nov-00 Release date: 17-Jan-01

Protein chain

P06213  (INSR_HUMAN) -  Insulin receptor from Homo sapiens

Seq: 1382 a.a.

Struc: 303 a.a.*

Protein chain

No UniProt id for this chain

Struc: 13 a.a.

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

Enzyme reactions

• Enzyme class: Chain A: E.C.2.7.10.1 - receptor protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

L-tyrosyl-[protein] (Bound ligand (Het Group name = 112) matches with 83.33% similarity) + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H(+)

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

Added reference

DOI no: 10.1038/83028

Nat Struct Biol 8:37-41 (2001)

PubMed id: 11135668

Mechanism-based design of a protein kinase inhibitor.

K.Parang, J.H.Till, A.J.Ablooglu, R.A.Kohanski, S.R.Hubbard, P.A.Cole.

ABSTRACT

Protein kinase inhibitors have applications as anticancer therapeutic agents and biological tools in cell signaling. Based on a phosphoryl transfer mechanism involving a dissociative transition state, a potent and selective bisubstrate inhibitor for the insulin receptor tyrosine kinase was synthesized by linking ATPgammaS to a peptide substrate analog via a two-carbon spacer. The compound was a high affinity competitive inhibitor against both nucleotide and peptide substrates and showed a slow off-rate. A crystal structure of this inhibitor bound to the tyrosine kinase domain of the insulin receptor confirmed the key design features inspired by a dissociative transition state, and revealed that the linker takes part in the octahedral coordination of an active site Mg2+. These studies suggest a general strategy for the development of selective protein kinase inhibitors.

Selected figure(s)

Figure 2.
Figure 2. Kinetic analysis of the inhibition of IRK by bisubstrate analog compound 2. a, E/V versus 1/ATP in the presence of varying concentrations of compound 2. b, E/V versus 1/IRS727 in the presence of varying compound 2. For (a), the apparent K[i] (compound 2) was 550 80 nM; for (b), the apparent K[i] (compound 2) was 750 90 nM. c, Product/Enzyme versus Time. This experiment monitors the phosphopeptide (product) formation after a rapid dilution of the enzyme -inhibitor complex to indirectly measure the k[off] for dissociation of compound 2 from IRK; k[off] = 0.013 0.001 s-1.

Figure 3.
Figure 3. Crystal structure of the binary complex between cIRK and the bisubstrate inhibitor. a, Overall view of the binary complex in which cIRK is shown in surface representation and the bisubstrate inhibitor in stick representation. The ATP S moiety of the inhibitor is colored green, the peptide moiety is colored red, and the linker connecting the nucleotide and peptide is colored yellow. The cIRK surface is semi-transparent; the N-terminal lobe of cIRK partially masks the nucleotide. b, Stereo view of the F[o] - F[c] electron density (2.7 Å resolution, 3 contour) for the bisubstrate inhibitor computed after simulated annealing (1,000 K), omitting from the atomic model either ATP S + linker (blue map) or the peptide moiety (green map). Coloring of the bisubstrate inhibitor is the same as in (a). Selected peptide residues are labeled; Y'(P0) refers to the modified Tyr at the P0 position of the peptide. The purple sphere represents the Mg2+ and the red sphere represents the Mg2+-coordinating water molecule. c, Stereo view of the interactions between the inhibitor and key catalytic residues. Superimposed are the cIRK -bisubstrate inhibitor (binary) complex and the cIRK -MgAMP-PNP -peptide (ternary) complex15. Oxygen atoms are colored red, nitrogen atoms blue, sulfur atoms green, and phosphorus atoms yellow. Bonds/carbon atoms are colored orange for the binary complex and green for the ternary complex. Bonds and atoms of the ternary complex are semi-transparent. Mg2+ ions and water molecules are represented as purple and red spheres, respectively. Hydrogen bonds and bonds to the Mg2+ are represented as dashed and solid black lines, respectively. Only the modified tyrosine from the peptide moiety of the inhibitor is shown. 'BSI' indicates the bisubstrate inhibitor in the binary complex, and 'Y(P0)' and 'PNP' indicate the substrate tyrosine and AMP-PNP, respectively, in the ternary complex. Selected secondary structural elements ( C and 3) are shown. The figure was prepared with GRASP28, BOBSCRIPT29 and MOLSCRIPT30.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 37-41) copyright 2001.

Figures were selected by an automated process.