5ITA

Crystal Structure of BRAF Kinase Domain Bound to AZ-VEM

• PDB DOI: https://doi.org/10.2210/pdb5ITA/pdb

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


• Deposited: 2016-03-16 Released: 2016-08-10 
• Deposition Author(s): Wu, Y., Gavathiotis, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.244 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.26 kDa 
• Atom Count: 4,177 
• Modelled Residue Count: 502 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	A, B	297	Homo sapiens	Mutation(s): 16  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
6DC	C [auth A], D [auth B]	N-{2-cyano-3-[(3-methyl-4-oxo-3,4-dihydroquinazolin-6-yl)amino]phenyl}propane-1-sulfonamide C19 H19 N5 O3 S VBLJFIYCXZTIPN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6DC	BindingDB:  5ITA	IC50: min: 0.3, max: 6 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.244 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.105	α = 90
b = 103.817	β = 90
c = 110.567	γ = 90

Software Package:

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

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: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description