4MBJ

Human B-Raf Kinase Domain in Complex with an Imidazopyridine-based Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4MBJ/pdb

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


• Deposited: 2013-08-19 Released: 2013-10-02 
• Deposition Author(s): Voegtli, W.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.328 
• R-Value Work: 0.276 
• R-Value Observed: 0.276 

Literature

Imidazo[4,5-b]pyridine inhibitors of B-Raf kinase.

Newhouse, B.J., Wenglowsky, S., Grina, J., Laird, E.R., Voegtli, W.C., Ren, L., Ahrendt, K., Buckmelter, A., Gloor, S.L., Klopfenstein, N., Rudolph, J., Wen, Z., Li, X., Feng, B.

(2013) Bioorg Med Chem Lett 23: 5896-5899

• PubMed: 24042006 
• DOI: https://doi.org/10.1016/j.bmcl.2013.08.086
• Primary Citation of Related Structures:  
  4MBJ


• PubMed Abstract: 
  

  This Letter details the synthesis and evaluation of imidazo[4,5-b]pyridines as inhibitors of B-Raf kinase. These compounds bind in a DFG-in, αC-helix out conformation of B-Raf, which is a binding mode associated with significant kinase selectivity. Structure-activity relationship studies involved optimization of the ATP-cleft binding region of these molecules, and led to compound 23, an inhibitor with excellent enzyme/cell potency, and kinase selectivity.

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Organizational Affiliation: 

Array BioPharma Inc., 3200 Walnut Street, Boulder, CO 80301, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 70.41 kDa 
• Atom Count: 4,420 
• Modelled Residue Count: 545 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	A, B	304	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
DFS	C [auth A], D [auth B]	2,6-difluoro-N-(1H-imidazo[4,5-b]pyridin-6-yl)-3-[(propylsulfonyl)amino]benzamide C16 H15 F2 N5 O3 S CWDHWLRBSAIDBH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DFS	PDBBind:  4MBJ	IC50: 61 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.328 
• R-Value Work: 0.276 
• R-Value Observed: 0.276 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.97	α = 90
b = 106.97	β = 90
c = 152.44	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Voegtli, W.C.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2013-11-06
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations