5CT7

BRAF in Complex with RAF265

PDB DOI: https://doi.org/10.2210/pdb5CT7/pdb

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

Deposited: 2015-07-23 Released: 2015-09-09
Deposition Author(s): Appleton, B.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.17 Å
R-Value Free: 0.217
R-Value Work: 0.181
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of RAF265: A Potent mut-B-RAF Inhibitor for the Treatment of Metastatic Melanoma.

Williams, T.E., Subramanian, S., Verhagen, J., McBride, C.M., Costales, A., Sung, L., Antonios-McCrea, W., McKenna, M., Louie, A.K., Ramurthy, S., Levine, B., Shafer, C.M., Machajewski, T., Renhowe, P.A., Appleton, B.A., Amiri, P., Chou, J., Stuart, D., Aardalen, K., Poon, D.

(2015) ACS Med Chem Lett 6: 961-965

PubMed: 26396681 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/ml500526p
Primary Citation of Related Structures:
5CT7

PubMed Abstract:
Abrogation of errant signaling along the MAPK pathway through the inhibition of B-RAF kinase is a validated approach for the treatment of pathway-dependent cancers. We report the development of imidazo-benzimidazoles as potent B-RAF inhibitors. Robust in vivo efficacy coupled with correlating pharmacokinetic/pharmacodynamic (PKPD) and PD-efficacy relationships led to the identification of RAF265, 1, which has advanced into clinical trials.

Organizational Affiliation

Global Discovery Chemistry, Oncology and Exploratory Chemistry, Novartis Institutes for Biomedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.

Macromolecule Content

Total Structure Weight: 64.86 kDa
Atom Count: 4,084
Modelled Residue Count: 511
Deposited Residue Count: 562
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	A, B	281	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15056
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
55J Query on 55J Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	1-methyl-5-({2-[5-(trifluoromethyl)-1H-imidazol-2-yl]pyridin-4-yl}oxy)-N-[4-(trifluoromethyl)phenyl]-1H-benzimidazol-2-amine C₂₄ H₁₆ F₆ N₆ O YABJJWZLRMPFSI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.17 Å
R-Value Free: 0.217
R-Value Work: 0.181
R-Value Observed: 0.183
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.38	α = 90
b = 109.38	β = 90
c = 158.13	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-09-09

Deposition Author(s):

Appleton, B.A.

Revision History (Full details and data files)

Version 1.0: 2015-09-09
Type: Initial release
Version 1.1: 2015-10-07
Changes: Database references
Version 1.2: 2024-03-06
Changes: Data collection, Database references, Derived calculations