PDBsum entry 3c4c

Transferase

PDB id: 3c4c

Contents

Protein chains

258 a.a. *

Ligands

324 ×2

Waters ×153

* Residue conservation analysis

PDB id:

3c4c

Name:

Transferase

Title:

B-raf kinase in complex with plx4720

Structure:

B-raf proto-oncogene serine/threonine-protein kinase. Chain: a, b. Fragment: kinase domain. Synonym: p94, v-raf murine sarcoma viral oncogene homolog b1. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: braf, braf1, rafb1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.57Å R-factor: 0.261 R-free: 0.303

Authors:

K.Y.J.Zhang,W.Wang

Key ref:

J.Tsai et al. (2008). Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity. Proc Natl Acad Sci U S A, 105, 3041-3046. PubMed id: 18287029 DOI: 10.1073/pnas.0711741105

Date:

29-Jan-08 Release date: 26-Feb-08

Protein chains

P15056  (BRAF_HUMAN) -  Serine/threonine-protein kinase B-raf from Homo sapiens

Seq: 766 a.a.

Struc: 258 a.a.*

* PDB and UniProt seqs differ at 15 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

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

reference

DOI no: 10.1073/pnas.0711741105

Proc Natl Acad Sci U S A 105:3041-3046 (2008)

PubMed id: 18287029

Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity.

J.Tsai, J.T.Lee, W.Wang, J.Zhang, H.Cho, S.Mamo, R.Bremer, S.Gillette, J.Kong, N.K.Haass, K.Sproesser, L.Li, K.S.Smalley, D.Fong, Y.L.Zhu, A.Marimuthu, H.Nguyen, B.Lam, J.Liu, I.Cheung, J.Rice, Y.Suzuki, C.Luu, C.Settachatgul, R.Shellooe, J.Cantwell, S.H.Kim, J.Schlessinger, K.Y.Zhang, B.L.West, B.Powell, G.Habets, C.Zhang, P.N.Ibrahim, P.Hirth, D.R.Artis, M.Herlyn, G.Bollag.

ABSTRACT

BRAF(V600E) is the most frequent oncogenic protein kinase mutation known. Furthermore, inhibitors targeting "active" protein kinases have demonstrated significant utility in the therapeutic repertoire against cancer. Therefore, we pursued the development of specific kinase inhibitors targeting B-Raf, and the V600E allele in particular. By using a structure-guided discovery approach, a potent and selective inhibitor of active B-Raf has been discovered. PLX4720, a 7-azaindole derivative that inhibits B-Raf(V600E) with an IC(50) of 13 nM, defines a class of kinase inhibitor with marked selectivity in both biochemical and cellular assays. PLX4720 preferentially inhibits the active B-Raf(V600E) kinase compared with a broad spectrum of other kinases, and potent cytotoxic effects are also exclusive to cells bearing the V600E allele. Consistent with the high degree of selectivity, ERK phosphorylation is potently inhibited by PLX4720 in B-Raf(V600E)-bearing tumor cell lines but not in cells lacking oncogenic B-Raf. In melanoma models, PLX4720 induces cell cycle arrest and apoptosis exclusively in B-Raf(V600E)-positive cells. In B-Raf(V600E)-dependent tumor xenograft models, orally dosed PLX4720 causes significant tumor growth delays, including tumor regressions, without evidence of toxicity. The work described here represents the entire discovery process, from initial identification through structural and biological studies in animal models to a promising therapeutic for testing in cancer patients bearing B-Raf(V600E)-driven tumors.

Selected figure(s)

Figure 1.
Structures of individual compounds leading to the discovery of PLX4720 are shown. (A) The chemical structure of 3-aminophenyl-7-azaindole (compound 1) is shown beneath its costructure with Pim-1 kinase. (B) The chemical structure of 3-(3-methoxybenzyl)-7-azaindole (compound 2) is shown beneath its costructure with the kinase domain of FGFR1. (C) The chemical structure of PLX4720 is shown beneath its costructure with B-Raf kinase.

Figure 2.
Depiction of the three-dimensional structure of PLX4720 bound to B-Raf. (A) The structure of B-Raf^V600E bound to PLX4720 (yellow) is overlayed with an ATP model based on structures of ATP analogs in complex with other tyrosine kinases (orange). This view indicates that the PLX4720 scaffold overlaps with the adenine-binding site, but the tail of PLX4720 binds to a different pocket from the ATP ribose-triphosphate tail. The positions of the hinge, activation loop (A-loop), and phosphate-binding loop (P-loop) are also shown. (B) A surface representation shows PLX4720 binding to the B-Raf-selective pocket in the active conformation. (C) A surface representation shows PLX4720 binding to the kinase general pocket in the inactive conformation. (D) A close-up view shows the overlay PLX4720 bound to both active (green) and inactive (purple) conformations of the V600 protein, and PLX3203 (yellow) bound to V600E protein in the active kinase conformation. (E) A stereoview shows the specific interactions of PLX4720 to the active kinase conformation. In this conformation, the phenylalanine of the DFG loop is pointing in toward the compound-binding site. (F) A stereoview shows the specific interactions of PLX4720 to the inactive kinase conformation. In this conformation, the phenylalanine of the DFG loop is pointing away from the compound-binding site, and binding of PLX4720 is disfavored, leading to partial occupancy of this site even at the 1 mM compound concentration used in cocrystallography.

Figures were selected by an automated process.