4IHL

Human 14-3-3 isoform zeta in complex with a diphoyphorylated C-RAF peptide and Cotylenin A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Stabilization of Physical RAF/14-3-3 Interaction by Cotylenin A as Treatment Strategy for RAS Mutant Cancers.

Molzan, M., Kasper, S., Roglin, L., Skwarczynska, M., Sassa, T., Inoue, T., Breitenbuecher, F., Ohkanda, J., Kato, N., Schuler, M., Ottmann, C.

(2013) ACS Chem Biol 8: 1869-1875

  • DOI: https://doi.org/10.1021/cb4003464
  • Primary Citation of Related Structures:  
    4IEA, 4IHL

  • PubMed Abstract: 

    • One-third of all human cancers harbor somatic RAS mutations. This leads to aberrant activation of downstream signaling pathways involving the RAF kinases. Current ATP-competitive RAF inhibitors are active in cancers with somatic RAF mutations, such as BRAF(V600) mutant melanomas ...

    One-third of all human cancers harbor somatic RAS mutations. This leads to aberrant activation of downstream signaling pathways involving the RAF kinases. Current ATP-competitive RAF inhibitors are active in cancers with somatic RAF mutations, such as BRAF(V600) mutant melanomas. However, they paradoxically promote the growth of RAS mutant tumors, partly due to the complex interplay between different homo- and heterodimers of A-RAF, B-RAF, and C-RAF. Based on pathway analysis and structure-guided compound identification, we describe the natural product cotylenin-A (CN-A) as stabilizer of the physical interaction of C-RAF with 14-3-3 proteins. CN-A binds to inhibitory 14-3-3 interaction sites of C-RAF, pSer233, and pSer259, but not to the activating interaction site, pSer621. While CN-A alone is inactive in RAS mutant cancer models, combined treatment with CN-A and an anti-EGFR antibody synergistically suppresses tumor growth in vitro and in vivo. This defines a novel pharmacologic strategy for treatment of RAS mutant cancers.

    Organizational Affiliation: 

    Chemical Genomics Centre of the Max-Planck-Society , Otto-Hahn-Strasse 15, 44227 Dortmund, Germany.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
14-3-3 protein zeta/deltaA, B235Homo sapiensMutation(s): 0 
Gene Names: YWHAZ
UniProt & NIH Common Fund Data Resources
Find proteins for P63104 (Homo sapiens)
Explore P63104 
Go to UniProtKB:  P63104
PHAROS:  P63104
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63104
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RAF proto-oncogene serine/threonine-protein kinaseC [auth P]36Homo sapiensMutation(s): 0 
Gene Names: RAF1, RAF
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04049 (Homo sapiens)
Explore P04049 
Go to UniProtKB:  P04049
PHAROS:  P04049
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04049
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1F5
Query on 1F5
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]		(1R,3aS,4R,5R,6R,9aR,10E)-6-({(1S,2R,4S,5R,6R,8S,9S)-5-hydroxy-2-(methoxymethyl)-9-methyl-9-[(2S)-oxiran-2-yl]-3,7,10,1 1-tetraoxatricyclo[6.2.1.0~1,6~]undec-4-yl}oxy)-1-(methoxymethyl)-4,9a-dimethyl-7-(propan-2-yl)-1,2,3,3a,4,5,6,8,9,9a-de cahydrodicyclopenta[a,d][8]annulene-1,5-diol
C33 H50 O11
SMQRKTIIIYTOTN-XWJJHAMOSA-N		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		C [auth P]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
1F5 BindingDB:  4IHL Kd: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.28α = 90
b = 103.4β = 90
c = 112.58γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
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: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references