6V2U | pdb_00006v2u

Crystal structure of the insect cell-expressed WT-BRAF kinase in complex with Dabrafenib

• PDB DOI: https://doi.org/10.2210/pdb6V2U/pdb

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


• Deposited: 2019-11-25 Released: 2020-12-02 
• Deposition Author(s): Li, K., Gonzalez Del-Pino, G., Park, E., Eck, M.J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.78 Å
• R-Value Free: 
  0.309 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.281 (Depositor), 0.277 (DCC) 
• R-Value Observed: 
  0.282 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the insect cell-expressed WT-BRAF kinase in complex with Dabrafenib

Li, K., Gonzalez Del-Pino, G., Park, E., Eck, M.J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 65.27 kDa 
• Atom Count: 4,107 
• Modeled Residue Count: 505 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	A, B	283	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
P06 (Subject of Investigation/LOI)	C [auth A], E [auth B]	Dabrafenib C23 H20 F3 N5 O2 S2 BFSMGDJOXZAERB-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
P06	BindingDB:  6V2U	IC50: min: 0.4, max: 11 (nM) from 15 assay(s)
		EC50: min: 0.7, max: 529 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.78 Å
• R-Value Free:  0.309 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.281 (Depositor), 0.277 (DCC) 
• R-Value Observed: 0.282 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.618	α = 90
b = 89.618	β = 90
c = 164.583	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Li, K., Gonzalez Del-Pino, G., Park, E., Eck, M.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P50 CA165962
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R50 CA221830
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35 CA242461

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description