6B8U | pdb_00006b8u

Crystals Structure of B-Raf kinase domain in complex with an Imidazopyridinyl benzamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6B8U/pdb

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


• Deposited: 2017-10-09 Released: 2017-11-22 
• Deposition Author(s): Appleton, B.A., Murray, J., Shafer, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.218 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Imidazo[1,2-a]pyridin-6-yl-benzamide analogs as potent RAF inhibitors.

Smith, A., Ni, Z.J., Poon, D., Huang, Z., Chen, Z., Zhang, Q., Tandeske, L., Merritt, H., Shoemaker, K., Chan, J., Kaufman, S., Huh, K., Murray, J., Appleton, B.A., Cowan-Jacob, S.W., Scheufler, C., Kanazawa, T., Jansen, J.M., Stuart, D., Shafer, C.M.

(2017) Bioorg Med Chem Lett 27: 5221-5224

• PubMed: 29107542 
• DOI: https://doi.org/10.1016/j.bmcl.2017.10.047
• Primary Citation Related Structures: 
  5MZ3, 6B8U


• PubMed Abstract: 
  

  A series of imidazo[1,2-a]pyridin-6-yl-benzamide analogs was designed as inhibitors of B-RAF ^V600E . Medicinal chemistry techniques were employed to explore the SAR for this series and improve selectivity versus P38 and VEGFR2.

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Organizational Affiliation: 
• Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, CA 94608, United States.
Novartis Institutes of Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland.
Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, CA 94608, United States. Electronic address: [e-mail].

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: 64.73 kDa 
• Atom Count: 4,121 
• Modeled Residue Count: 501 
• Deposited Residue Count: 562 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	A, B	281	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
8EN	C [auth A], D [auth B]	~{N}-[3-(2-acetamidoimidazo[1,2-a]pyridin-6-yl)-4-methyl-phenyl]-3-(trifluoromethyl)benzamide C24 H19 F3 N4 O2 MRTHXFZEQBERDI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free:  0.218 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.502	α = 90
b = 93.502	β = 90
c = 164.703	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PROCESS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-22 
Deposition Author(s): Appleton, B.A., Murray, J., Shafer, C.M.

Revision History  

• Version 1.0: 2017-11-22
  Type: Initial release
  
• Version 1.1: 2017-11-29
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description