Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.48 kDa 
• Atom Count: 4141 
• Modelled Residue Count: 498 
• Deposited Residue Count: 556 
• Unique protein chains: 1

4CQE

B-Raf Kinase V600E mutant in complex with a diarylthiazole B-Raf Inhibitor

• DOI: 10.2210/pdb4CQE/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-02-14 Released: 2014-12-10 
• Deposition Author(s): Casale, E., Fasolini, M., Pulici, M., Traquandi, G., Marchionni, C., Modugno, M., Lupi, R., Amboldi, N., Colombo, N., Corti, L., Gasparri, F., Pastori, W., Scolaro, A., Donati, D., Felder, E., Galvani, A., Isacchi, A., Pesenti, E., Ciomei, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.255 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

Optimization of Diarylthiazole B-Raf Inhibitors: Identification of a Compound Endowed with High Oral Antitumor Activity, Mitigated Herg Inhibition, and Low Paradoxical Effect.

Pulici, M., Traquandi, G., Marchionni, C., Modugno, M., Lupi, R., Amboldi, N., Casale, E., Colombo, N., Corti, L., Fasolini, M., Gasparri, F., Pastori, W., Scolaro, A., Donati, D., Felder, E., Galvani, A., Isacchi, A., Pesenti, E., Ciomei, M.

(2015) ChemMedChem 10: 276

• PubMed: 25430902 
• DOI: 10.1002/cmdc.201402424
• Primary Citation of Related Structures:  
  4CQE


• PubMed Abstract: 
  

Aberrant activation of the mitogen-activated protein kinase (MAPK)-mediated pathway components, RAF-MEK-ERK, is frequently observed in human cancers and clearly contributes to oncogenesis. As part of a project aimed at finding inhibitors of B-Raf, a key player in the MAPK cascade, we originally identified a thiazole derivative endowed with high potency and selectivity, optimal in vitro ADME properties, and good pharmacokinetic profiles in rodents, but that suffers from elevated hERG inhibitory activity. An optimization program was thus undertaken, focused mainly on the elaboration of the R(1) and R(2) groups of the scaffold. This effort ultimately led to N-(4-{2-(1-cyclopropylpiperidin-4-yl)-4-[3-(2,5-difluorobenzenesulfonylamino)-2-fluorophenyl]thiazol-5-yl}-pyridin-2-yl)acetamide (20), which maintains favorable in vitro and in vivo properties, but lacks hERG liability. Besides exhibiting potent antiproliferative activity against only cell lines bearing B-Raf V600E or V600D mutations, compound 20 also intriguingly shows a weaker "paradoxical" activation of MEK in non-mutant B-Raf cells than other known B-Raf inhibitors. It also demonstrates very good efficacy in vivo against the A375 xenograft melanoma model (tumor volume inhibition >90% at 10 mg kg(-1) ); it is therefore a suitable candidate for preclinical development.

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Organizational Affiliation: 

Nerviano Medical Sciences Srl, Business Unit Oncology, Viale Pasteur 10, 20014 Nerviano (MI) (Italy). [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SLC45A3-BRAF FUSION PROTEIN	A, B	278	Homo sapiens	Mutation(s): 17  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
CQE (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-{4-[2-(1-cyclopropylpiperidin-4-yl)-4-(3-{[(2,5-difluorophenyl)sulfonyl]amino}-2-fluorophenyl)-1,3-thiazol-5-yl]pyridin-2-yl}acetamide C30 H28 F3 N5 O3 S2 WXOCHOSJBRDQIZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CQE	Binding MOAD:  4CQE	Kd: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.255 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.605	α = 90
b = 105.943	β = 90
c = 109.889	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2014-02-14 
• Released Date: 2014-12-10 
Deposition Author(s): Casale, E., Fasolini, M., Pulici, M., Traquandi, G., Marchionni, C., Modugno, M., Lupi, R., Amboldi, N., Colombo, N., Corti, L., Gasparri, F., Pastori, W., Scolaro, A., Donati, D., Felder, E., Galvani, A., Isacchi, A., Pesenti, E., Ciomei, M.

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2015-02-11
  Changes: Database references
• Version 1.2: 2018-02-28
  Changes: Data collection
• Version 1.3: 2019-01-30
  Changes: Data collection, Experimental preparation