9BFB

Crystal structure of BRAF kinase domain with PF-07284890


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Identification of the Clinical Candidate PF-07284890 ( ARRY-461 ), a Highly Potent and Brain Penetrant BRAF Inhibitor for the Treatment of Cancer.

Ren, L.Moreno, D.Baer, B.R.Barbour, P.Bettendorf, T.Bouhana, K.Brown, K.Brown, S.A.Fell, J.B.Hartley, D.P.Hicken, E.J.Laird, E.R.Lee, P.McCown, J.Otten, J.N.Prigaro, B.Wallace, R.Kahn, D.

(2024) J Med Chem 67: 13019-13032

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00998
  • Primary Citation of Related Structures:  
    9BFB

  • PubMed Abstract: 

    Mutant BRAF V600E is one of the most common oncogenic drivers in metastatic melanoma. While first generation BRAF V600E inhibitors are capable of controlling tumors systemically, they are unable to adequately treat tumors that have metastasized to the brain due to insufficient penetration across the blood-brain barrier (BBB). Through a combination of structure-based drug design (SBDD) and the optimization of physiochemical properties to enhance BBB penetration, we herein report the discovery of the brain-penetrant BRAF V600E inhibitor PF-07284890 ( ARRY-461 ) . In mice studies, ARRY-461 proved to be highly brain-penetrant and was able to drive regressions of A375 BRAF V600E tumors implanted both subcutaneously and intracranially. Based on compelling preclinical safety and efficacy studies, ARRY-461 was progressed into a Phase 1 A/B clinical trial (NCT04543188).


  • Organizational Affiliation

    Enliven Therapeutics, Boulder, Colorado 80301, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf294Homo sapiensMutation(s): 3 
Gene Names: BRAFBRAF1RAFB1
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AN9 (Subject of Investigation/LOI)
Query on A1AN9

Download Ideal Coordinates CCD File 
D [auth A]N-{2-chloro-3-[(3,5-dimethyl-4-oxo-3,4-dihydroquinazolin-6-yl)amino]-4-fluorophenyl}-3-fluoropropane-1-sulfonamide
C19 H19 Cl F2 N4 O3 S
VVLVISDSGRHLMB-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
B [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.609α = 90
b = 97.609β = 90
c = 69.311γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-08-14 
  • Deposition Author(s): Mou, T.-C.

Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release