Experimental Data Snapshot

  • Resolution: 2.51 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.223 

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This is version 1.4 of the entry. See complete history


A Novel RAF Kinase Inhibitor with DFG-Out-Binding Mode: High Efficacy in BRAF-Mutant Tumor Xenograft Models in the Absence of Normal Tissue Hyperproliferation.

Waizenegger, I.C.Baum, A.Steurer, S.Stadtmuller, H.Bader, G.Schaaf, O.Garin-Chesa, P.Schlattl, A.Schweifer, N.Haslinger, C.Colbatzky, F.Mousa, S.Kalkuhl, A.Kraut, N.Adolf, G.R.

(2016) Mol Cancer Ther 15: 354-365

  • DOI: https://doi.org/10.1158/1535-7163.MCT-15-0617
  • Primary Citation of Related Structures:  
    5CSW, 5CSX

  • PubMed Abstract: 

    BI 882370 is a highly potent and selective RAF inhibitor that binds to the DFG-out (inactive) conformation of the BRAF kinase. The compound inhibited proliferation of human BRAF-mutant melanoma cells with 100× higher potency (1-10 nmol/L) than vemurafenib, whereas wild-type cells were not affected at 1,000 nmol/L. BI 882370 administered orally was efficacious in multiple mouse models of BRAF-mutant melanomas and colorectal carcinomas, and at 25 mg/kg twice daily showed superior efficacy compared with vemurafenib, dabrafenib, or trametinib (dosed to provide exposures reached in patients). To model drug resistance, A375 melanoma-bearing mice were initially treated with vemurafenib; all tumors responded with regression, but the majority subsequently resumed growth. Trametinib did not show any efficacy in this progressing population. BI 882370 induced tumor regression; however, resistance developed within 3 weeks. BI 882370 in combination with trametinib resulted in more pronounced regressions, and resistance was not observed during 5 weeks of second-line therapy. Importantly, mice treated with BI 882370 did not show any body weight loss or clinical signs of intolerability, and no pathologic changes were observed in several major organs investigated, including skin. Furthermore, a pilot study in rats (up to 60 mg/kg daily for 2 weeks) indicated lack of toxicity in terms of clinical chemistry, hematology, pathology, and toxicogenomics. Our results indicate the feasibility of developing novel compounds that provide an improved therapeutic window compared with first-generation BRAF inhibitors, resulting in more pronounced and long-lasting pathway suppression and thus improved efficacy.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf282Homo sapiensMutation(s): 15 
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
GTEx:  ENSG00000157764 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 54J

Download Ideal Coordinates CCD File 
B [auth A]N-(3-{5-[(1-ethylpiperidin-4-yl)(methyl)amino]-3-(pyrimidin-5-yl)-1H-pyrrolo[3,2-b]pyridin-1-yl}-2,4-difluorophenyl)propane-1-sulfonamide
C28 H33 F2 N7 O2 S
Query on GLC

Download Ideal Coordinates CCD File 
C [auth A]alpha-D-glucopyranose
C6 H12 O6
Binding Affinity Annotations 
IDSourceBinding Affinity
54J BindingDB:  5CSX Kd: min: 0.33, max: 0.37 (nM) from 2 assay(s)
IC50: min: 0.4, max: 0.8 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.51 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.223 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.375α = 90
b = 116.136β = 90
c = 102.423γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2018-04-25
    Changes: Advisory, Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-01-10
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary