5C9C

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    5C9C

  • 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 vemurafenib or dabrafenib have little or modest CRAF activity compared to their BRAF activities ...

    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: 

    Deciphera Pharmaceuticals, LLC, Lawrence, KS 66044, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-rafA, B307Homo sapiensMutation(s): 1 
Gene Names: BRAF, BRAF1, RAFB1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
PHAROS:  P15056
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4Z5
Query on 4Z5
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		1-(3,3-dimethylbutyl)-3-{2-fluoro-4-methyl-5-[7-methyl-2-(methylamino)pyrido[2,3-d]pyrimidin-6-yl]phenyl}urea
C23 H29 F N6 O
HHCBMISMPSAZBF-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
E [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4Z5 BindingDB:  5C9C Ki: 0.14 (nM) from 1 assay(s)
IC50: min: 1.5, max: 5800 (nM) from 7 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.88α = 90
b = 93.88β = 90
c = 165.55γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
Cootmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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