4RZV

Crystal structure of the BRAF (R509H) kinase domain monomer bound to Vemurafenib

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf
A, B
281Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
032
Query on 032
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		N-(3-{[5-(4-chlorophenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]carbonyl}-2,4-difluorophenyl)propane-1-sulfonamide
C23 H18 Cl F2 N3 O3 S
GPXBXXGIAQBQNI-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
032 BindingDB:  4RZV Kd: min: 51, max: 58 (nM) from 2 assay(s)
IC50: min: 4, max: 3.30e+4 (nM) from 33 assay(s)
EC50: min: 601, max: 2290 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.975α = 90
b = 71.698β = 90
c = 243.281γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Structure summary
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary