Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 94474.90 
• Atom Count: 6417 
• Residue Count: 825 
• Unique protein chains: 1

4H58

BRAF in complex with compound 3

• DOI: 10.2210/pdb4H58/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• 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: 3.1 Å
• R-Value Free: 0.272 
• R-Value Work: 0.222 

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: 10.1021/jm301658d
• Primary Citation of Related Structures:  
  4BB4


• 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]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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
Find proteins for P15056 (Homo sapiens) Go to Gene View: BRAF Go to UniProtKB:  P15056

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
10Z	A	N-(4-{[(2-methoxyethyl)amino]methyl}phenyl)-6-(pyridin-4-yl)quinazolin-2-amine C23 H23 N5 O UKKAXPVDQSQDFB-UHFFFAOYSA-N
CL	C	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
10Z	IC50: 192 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.1 Å
• R-Value Free: 0.272 
• R-Value Work: 0.222 
• Space Group: I 4₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 204.740	α = 90.00
b = 204.740	β = 90.00
c = 152.950	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-09-18 
• 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
  Type: Database references
• Version 1.2: 2017-11-15
  Type: Refinement description