4RZW | pdb_00004rzw

Crystal structure of BRAF (R509H) kinase domain bound to AZ628

PDB DOI: https://doi.org/10.2210/pdb4RZW/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-12-24 Released: 2016-08-10
Deposition Author(s): Wu, Y., Gavathiotis, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.49 Å
R-Value Free:
0.280 (Depositor), 0.277 (DCC)
R-Value Work:
0.247 (Depositor), 0.240 (DCC)
R-Value Observed:
0.248 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 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

Macromolecule Content

Total Structure Weight: 64.93 kDa
Atom Count: 4,100
Modeled Residue Count: 503
Deposited Residue Count: 562
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	A, B	281	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15056
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B1E Query on B1E 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]	3-(2-cyanopropan-2-yl)-N-{4-methyl-3-[(3-methyl-4-oxo-3,4-dihydroquinazolin-6-yl)amino]phenyl}benzamide C₂₇ H₂₅ N₅ O₂ ZGBGPEDJXCYQPH-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]

Binding Affinity Annotations
ID	Source	Binding Affinity
B1E	BindingDB: 4RZW	IC50: min: 0.6, max: 2640 (nM) from 8 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.49 Å
R-Value Free: 0.280 (Depositor), 0.277 (DCC)
R-Value Work: 0.247 (Depositor), 0.240 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.077	α = 90
b = 114.823	β = 90
c = 56.444	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Gavathiotis, E.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.