3PSB

Furo[2,3-c]pyridine-based Indanone Oximes as Potent and Selective B-Raf Inhibitors

• PDB DOI:  https://doi.org/10.2210/pdb3PSB/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-12-01 Released: 2011-01-19 
• Deposition Author(s): Morales, T., Vigers, G.P.A., Brandhuber, B.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.268 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Literature

The Discovery of furo[2,3-c]pyridine-based indanone oximes as potent and selective B-Raf inhibitors.

Buckmelter, A.J., Ren, L., Laird, E.R., Rast, B., Miknis, G., Wenglowsky, S., Schlachter, S., Welch, M., Tarlton, E., Grina, J., Lyssikatos, J., Brandhuber, B.J., Morales, T., Randolph, N., Vigers, G., Martinson, M., Callejo, M.

(2011) Bioorg Med Chem Lett 21: 1248-1252

• PubMed: 21211972 
• DOI: https://doi.org/10.1016/j.bmcl.2010.12.039
• Primary Citation of Related Structures:  
  3PSB


• PubMed Abstract: 
  

Virtual and high-throughput screening identified imidazo[1,2-a]pyrazines as inhibitors of B-Raf. We describe the rationale, SAR, and evolution of the initial hits to a series of furo[2,3-c]pyridine indanone oximes as highly potent and selective inhibitors of B-Raf.

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Organizational Affiliation: 

Array BioPharma, 3200 Walnut Street, Boulder, CO 80301, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.17 kDa 
• Atom Count: 4,252 
• Modelled Residue Count: 526 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE	A, B	307	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SM6	C [auth A], D [auth B]	ethyl 3-{[1-(hydroxyamino)-2H-inden-5-yl]amino}thieno[2,3-c]pyridine-2-carboxylate C19 H17 N3 O3 S CROUIRAPWZHAFI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SM6	PDBBind:  3PSB	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.268 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.073	α = 90
b = 101.073	β = 90
c = 162.952	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Morales, T., Vigers, G.P.A., Brandhuber, B.J.

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description