3PPK

Human B-Raf Kinase in Complex with a Non-Oxime Furopyridine Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3PPK/pdb

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


• Deposited: 2010-11-24 Released: 2011-02-02 
• Deposition Author(s): Voegtli, W.C., Vigers, G.P.A., Morales, T., Brandhuber, B.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.280 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 

Literature

Non-oxime inhibitors of B-Raf(V600E) kinase.

Ren, L., Wenglowsky, S., Miknis, G., Rast, B., Buckmelter, A.J., Ely, R.J., Schlachter, S., Laird, E.R., Randolph, N., Callejo, M., Martinson, M., Galbraith, S., Brandhuber, B.J., Vigers, G., Morales, T., Voegtli, W.C., Lyssikatos, J.

(2011) Bioorg Med Chem Lett 21: 1243-1247

• PubMed: 21251822 
• DOI: https://doi.org/10.1016/j.bmcl.2010.12.061
• Primary Citation of Related Structures:  
  3PPJ, 3PPK, 3PRF, 3PRI


• PubMed Abstract: 
  

  The development of inhibitors of B-Raf(V600E) serine-threonine kinase is described. Various head-groups were examined to optimize inhibitor activity and ADME properties. Several of the head-groups explored, including naphthol, phenol and hydroxyamidine, possessed good activity but had poor pharmacokinetic exposure in mice. Exposure was improved by incorporating more metabolically stable groups such as indazole and tricyclic pyrazole, while indazole could also be optimized for good cellular activity.

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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: 71.23 kDa 
• Atom Count: 4,260 
• Modelled Residue Count: 526 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	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 GTEx:  ENSG00000157764

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FNI	C [auth A], D [auth B]	3-[(5-hydroxynaphthalen-2-yl)amino]-N-(pyrimidin-4-yl)furo[2,3-c]pyridine-2-carboxamide C22 H15 N5 O3 AHLQDZCJPCLDJM-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FNI	PDBBind:  3PPK	IC50: 1.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.280 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.311	α = 90
b = 100.311	β = 90
c = 163.354	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-02 
Deposition Author(s): Voegtli, W.C., Vigers, G.P.A., Morales, T., Brandhuber, B.J.

Revision History  

• Version 1.0: 2011-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations