4RZW

Crystal structure of BRAF (R509H) kinase domain bound to AZ628

• PDB DOI: https://doi.org/10.2210/pdb4RZW/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-12-24 Released: 2016-08-10 
• Deposition Author(s): Wu, Y., Gavathiotis, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free: 0.280 
• R-Value Work: 0.247 
• R-Value Observed: 0.248 

Starting Model: experimental

Literature

An integrated model of RAF inhibitor action predicts inhibitor activity against oncogenic BRAF signaling

Karoulia, Z., Wu, Y., Ahmed, T.A., Qisheng, X., Bollard, J., Krepler, C., Wu, X., Zhang, C., Bollag, G., Herlym, M., Fagin, J.A., Lujambio, A., Gavathiotis, E., Poulikakos, P.I.

(2016) Cancer Cell 30: 1-14

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.93 kDa 
• Atom Count: 4,100 
• Modelled Residue Count: 503 
• 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): 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
B1E	C [auth A], D [auth B]	3-(2-cyanopropan-2-yl)-N-{4-methyl-3-[(3-methyl-4-oxo-3,4-dihydroquinazolin-6-yl)amino]phenyl}benzamide C27 H25 N5 O2 ZGBGPEDJXCYQPH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B1E	BindingDB:  4RZW	IC50: min: 0.6, max: 2640 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free: 0.280 
• R-Value Work: 0.247 
• R-Value Observed: 0.248 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.077	α = 90
b = 114.823	β = 90
c = 56.444	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Wu, Y., Gavathiotis, E.

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description