9BFB: BRAF kinase domain with PF-07284890

Crystal structure of BRAF kinase domain with PF-07284890. Determined by X-ray diffraction at 1.92 Å resolution. Released 14 Aug 2024.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,503
Mol. weight: 33.86 kDa
Ligands: A1AN9
Released: 14 Aug 2024

Explore 9BFB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BFB contains 17 α-helices and 10 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	451	1	1
α-helix	452-453	2
β-strand	458-465	8	1
β-strand	470-475	6	1
β-strand	479-484	6	1
α-helix	492-505	14
β-strand	513	1	2
β-strand	516-520	5	1
β-strand	526-530	5	1
α-helix	531-532	2
β-strand	534-536	3	2
α-helix	537-538	2
α-helix	539-543	5
α-helix	550-569	20
α-helix	579-581	3
β-strand	582-585	4	2
β-strand	589-592	4	2
α-helix	598-603	6
α-helix	609-616	8
α-helix	617-619	3
α-helix	622-626	5
α-helix	635-651	17
α-helix	662-670	9
α-helix	678-680	3
α-helix	687-696	10
α-helix	701-703	3
α-helix	707-718	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase B-raf	A	protein	294	Homo sapiens	P15056 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9BFB_1 Serine/threonine-protein kinase B-raf (chains A)
MGHHHHHHGLVPRGSDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTA
PTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFE
MIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQ
FEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIAMV
GAGALSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPK

Ligands and cofactors

ID	Name	Formula	Copies
A1AN9	N-{2-chloro-3-[(3,5-dimethyl-4-oxo-3,4-dihydroquinazolin-6-yl)amino]-4-fluoroph…	C19 H19 Cl F2 N4 O3 S	1

Water and common crystallization additives (PEG, GOL) are not listed.

Primary citation

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. et al. J Med Chem (2024) 67:13019-13032. DOI 10.1021/acs.jmedchem.4c00998 · PubMed

Other PDB entries of the same protein (UniProt P15056 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8VSO 1.5 Å, Ternary structure of 14-3-3 sigma, BRAF phosphopeptide (pS365) and compound 78 (1124378)
8JNB 1.62 Å, CRAF ras-binding domain chimera, ligand complex
8C7X 1.65 Å, Crystal structure of BRAF in complex with a hybrid compound 6
8C7Y 1.65 Å, Crystal structure of BRAF V600E in complex with a hybrid compound 6
9EW6 1.65 Å, Binary structure of 14-3-3s and BRAF phosphopeptide (pS365)
8JNA 1.7 Å, CRAF ras-binding domain chimera, apo form
9BP8 1.73 Å, Crystal structure of BRAF kinase domain with PF-07799933
5VYK 1.75 Å, Crystal structure of the BRS domain of BRAF in complex with the CC-SAM domain of KSR1
7K0V 1.93 Å, Crystal structure of bRaf in complex with inhibitor GNE-0749
5ITA 1.95 Å, Crystal Structure of BRAF Kinase Domain Bound to AZ-VEM
3NY5 1.99 Å, Crystal structure of the RBD domain of serine/threonine-protein kinase B-raf from Homo…
4XV9 2.0 Å, B-Raf Kinase domain in complex with PLX5568

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