3C4E

Pim-1 Kinase Domain in Complex with 3-aminophenyl-7-azaindole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

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

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

  • DOI: 10.1073/pnas.0711741105
  • Primary Citation of Related Structures:  
    4FK3, 3C4C, 3C4E, 3C4F

  • PubMed 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 develop ...

    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.


    Organizational Affiliation

    Plexxikon, Inc., 91 Bolivar Drive, Berkeley, CA 94710, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene serine/threonine-protein kinase Pim-1ABCD273Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
NIH Common Fund Data Resources
PHAROS  P11309
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C4E
Query on C4E

Download CCD File 
A, B, C, D
N-phenyl-1H-pyrrolo[2,3-b]pyridin-3-amine
C13 H11 N3
CQFGXDQUQWRXLE-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download CCD File 
A, B, C, D
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C4EIC50:  100000   nM  Binding MOAD
C4EIC50 :  100000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.455α = 90
b = 197.455β = 90
c = 80.679γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance