5C9C

CRYSTAL STRUCTURE OF BRAF(V600E) IN COMPLEX WITH LY3009120 COMPND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibition of RAF Isoforms and Active Dimers by LY3009120 Leads to Anti-tumor Activities in RAS or BRAF Mutant Cancers.

Peng, S.B.Henry, J.R.Kaufman, M.D.Lu, W.P.Smith, B.D.Vogeti, S.Rutkoski, T.J.Wise, S.Chun, L.Zhang, Y.Van Horn, R.D.Yin, T.Zhang, X.Yadav, V.Chen, S.H.Gong, X.Ma, X.Webster, Y.Buchanan, S.Mochalkin, I.Huber, L.Kays, L.Donoho, G.P.Walgren, J.McCann, D.Patel, P.Conti, I.Plowman, G.D.Starling, J.J.Flynn, D.L.

(2015) Cancer Cell 28: 384-398

  • DOI: 10.1016/j.ccell.2015.08.002

  • PubMed Abstract: 
  • LY3009120 is a pan-RAF and RAF dimer inhibitor that inhibits all RAF isoforms and occupies both protomers in RAF dimers. Biochemical and cellular analyses revealed that LY3009120 inhibits ARAF, BRAF, and CRAF isoforms with similar affinity, while vem ...

    LY3009120 is a pan-RAF and RAF dimer inhibitor that inhibits all RAF isoforms and occupies both protomers in RAF dimers. Biochemical and cellular analyses revealed that LY3009120 inhibits ARAF, BRAF, and CRAF isoforms with similar affinity, while vemurafenib or dabrafenib have little or modest CRAF activity compared to their BRAF activities. LY3009120 induces BRAF-CRAF dimerization but inhibits the phosphorylation of downstream MEK and ERK, suggesting that it effectively inhibits the kinase activity of BRAF-CRAF heterodimers. Further analyses demonstrated that LY3009120 also inhibits various forms of RAF dimers including BRAF or CRAF homodimers. Due to these unique properties, LY3009120 demonstrates minimal paradoxical activation, inhibits MEK1/2 phosphorylation, and exhibits anti-tumor activities across multiple models carrying KRAS, NRAS, or BRAF mutation.


    Related Citations: 
    • Discovery of 1-(3,3-dimethylbutyl)-3-(2-fluoro-4-methyl-5-(7-methyl-2-(methylamino)pyrido[2,3-d]pyrimidin-6-yl)phenyl)urea (LY3009120) as a pan-RAF inhibitor with minimal paradoxical activation and activity against BRAF or RAS mutant tumor cells.
      Henry, J.R.,Kaufman, M.D.,Peng, S.B.,Ahn, Y.M.,Caldwell, T.M.,Vogeti, L.,Telikepalli, H.,Lu, W.P.,Hood, M.M.,Rutkoski, T.J.,Smith, B.D.,Vogeti, S.,Miller, D.,Wise, S.C.,Chun, L.,Zhang, X.,Zhang, Y.,Kays, L.,Hipskind, P.A.,Wrobleski, A.D.,Lobb, K.L.,Clay, J.M.,Cohen, J.D.,Walgren, J.L.,McCann, D.,Patel, P.,Clawson, D.K.,Guo, S.,Manglicmot, D.,Groshong, C.,Logan, C.,Starling, J.J.,Flynn, D.L.
      (2015) J.Med.Chem. 58: 4165


    Organizational Affiliation

    Eli Lilly and Company, Indianapolis, IN 46285, USA. Electronic address: peng_sheng-bin@lilly.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase B-raf
A, B
307Homo sapiensMutation(s): 1 
Gene Names: BRAF (BRAF1, RAFB1)
EC: 2.7.11.1
Find proteins for P15056 (Homo sapiens)
Go to Gene View: BRAF
Go to UniProtKB:  P15056
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
4Z5
Query on 4Z5

Download SDF File 
Download CCD File 
A, B
1-(3,3-dimethylbutyl)-3-{2-fluoro-4-methyl-5-[7-methyl-2-(methylamino)pyrido[2,3-d]pyrimidin-6-yl]phenyl}urea
LY3009120
C23 H29 F N6 O
HHCBMISMPSAZBF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4Z5IC50: 5.8 - 37 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.880α = 90.00
b = 93.880β = 90.00
c = 165.550γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
REFMACrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-10-14
    Type: Database references