6XFP: BRAF kinase domain

Crystal Structure of BRAF kinase domain bound to Belvarafenib. Determined by X-ray diffraction at 2.0 Å resolution. Released 10 Mar 2021.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,333
Mol. weight: 33.52 kDa
Ligands: V1Y
Released: 10 Mar 2021

Explore 6XFP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XFP contains 15 α-helices and 14 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: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	451	1	1
α-helix	452-453	2
β-strand	458-466	9	1
β-strand	469-475	7	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
β-strand	534-536	3	2
α-helix	537-542	6
α-helix	550-569	20
α-helix	579-581	3
β-strand	582-585	4	2
β-strand	589-592	4	2
β-strand	597	1	3
β-strand	601	1	3
α-helix	602-604	3
β-strand	605	1	4
β-strand	608	1	4
α-helix	617-619	3
α-helix	622-626	5
α-helix	635-651	17
α-helix	662-671	10
α-helix	678-680	3
α-helix	687-696	10
α-helix	701-703	3
α-helix	705-706	2
α-helix	707-719	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase B-raf	A	protein	288	Homo sapiens	P15056 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6XFP_1 Serine/threonine-protein kinase B-raf (chains A)
MHHHHHGSRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQL
QAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYKHLHASETKFEMKKLID
IARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATVKSRWSGSHQFEQLSG
SILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLS
PDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELSG

Ligands and cofactors

ID	Name	Formula	Copies
V1Y	4-amino-N-{1-[(3-chloro-2-fluorophenyl)amino]-6-methylisoquinolin-5-yl}thieno[3…	C23 H16 Cl F N6 O S	1

Water and common crystallization additives (CL) are not listed.

Primary citation

ARAF mutations confer resistance to the RAF inhibitor belvarafenib in melanoma. Yen, I., Shanahan, F., Lee, J. et al. Nature (2021) 594:418-423. DOI 10.1038/s41586-021-03515-1 · 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
9BFB 1.92 Å, Crystal structure of BRAF kinase domain with PF-07284890
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…

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