4H58 | pdb_00004h58

BRAF in complex with compound 3

• PDB DOI: https://doi.org/10.2210/pdb4H58/pdb

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


• Deposited: 2012-09-18 Released: 2013-02-27 
• Deposition Author(s): Vasbinder, M., Aquila, B., Augustin, M., Chueng, T., Cook, D., Drew, L., Fauber, B., Glossop, S., Godin, R., Grondine, M., Hennessy, E., Johannes, J., Lee, S., Lyne, P., Moertl, M., Omer, C., Palakurthi, S., Pontz, T., Read, J., Sha, L., Shen, M., Steinbacher, S., Wang, H., Wu, A., Ye, M., Bagal, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.272 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Discovery and Optimization of a Novel Series of Potent Mutant B-Raf(V600E) Selective Kinase Inhibitors.

Vasbinder, M.M., Aquila, B., Augustin, M., Chen, H., Cheung, T., Cook, D., Drew, L., Fauber, B.P., Glossop, S., Grondine, M., Hennessy, E., Johannes, J., Lee, S., Lyne, P., Mortl, M., Omer, C., Palakurthi, S., Pontz, T., Read, J., Sha, L., Shen, M., Steinbacher, S., Wang, H., Wu, A., Ye, M.

(2013) J Med Chem 56: 1996-2015

• PubMed: 23398453 
• DOI: https://doi.org/10.1021/jm301658d
• Primary Citation Related Structures: 
  4BB4, 4H58


• PubMed Abstract: 
  

  B-Raf represents an attractive target for anticancer therapy and the development of small molecule B-Raf inhibitors has delivered new therapies for metastatic melanoma patients. We have discovered a novel class of small molecules that inhibit mutant B-Raf(V600E) kinase activity both in vitro and in vivo. Investigations into the structure-activity relationships of the series are presented along with efforts to improve upon the cellular potency, solubility, and pharmacokinetic profile. Compounds selectively inhibited B-Raf(V600E) in vitro and showed preferential antiproliferative activity in mutant B-Raf(V600E) cell lines and exhibited selectivity in a kinase panel against other kinases. Examples from this series inhibit growth of a B-Raf(V600E) A375 xenograft in vivo at a well-tolerated dose. In addition, aminoquinazolines described herein were shown to display pERK elevation in nonmutant B-Raf cell lines in vitro.

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Organizational Affiliation: 
• Oncology iMED, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.47 kDa 
• Atom Count: 6,432 
• Modeled Residue Count: 797 
• Deposited Residue Count: 825 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	A, B, C	275	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
10Z	D [auth A]	N-(4-{[(2-methoxyethyl)amino]methyl}phenyl)-6-(pyridin-4-yl)quinazolin-2-amine C23 H23 N5 O UKKAXPVDQSQDFB-UHFFFAOYSA-N
CL	E [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.272 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.74	α = 90
b = 204.74	β = 90
c = 152.95	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-27 
Deposition Author(s): Vasbinder, M., Aquila, B., Augustin, M., Chueng, T., Cook, D., Drew, L., Fauber, B., Glossop, S., Godin, R., Grondine, M., Hennessy, E., Johannes, J., Lee, S., Lyne, P., Moertl, M., Omer, C., Palakurthi, S., Pontz, T., Read, J., Sha, L., Shen, M., Steinbacher, S., Wang, H., Wu, A., Ye, M., Bagal, B.

Revision History  

• Version 1.0: 2013-02-27
  Type: Initial release
  
• Version 1.1: 2013-03-27
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description