5VAM: BRAF

BRAF in Complex with RAF709. Determined by X-ray diffraction at 2.1 Å resolution. Released 28 Jun 2017.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,582
Mol. weight: 64.91 kDa
Ligands: 92J
Released: 28 Jun 2017

Explore 5VAM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VAM contains 30 α-helices and 20 β-strands across 2 chains. 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, 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	469-475	7	1
β-strand	479-485	7	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	537-538	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	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	707-720	14

Chain B: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	451	1	3
α-helix	452-453	2
β-strand	458-465	8	3
β-strand	469-475	7	3
β-strand	479-485	7	3
α-helix	492-505	14
β-strand	513	1	4
β-strand	516-520	5	3
β-strand	526-530	5	3
β-strand	534-536	3	4
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	4
β-strand	589-592	4	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, B	protein	281	Homo sapiens	P15056 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5VAM_1 Serine/threonine-protein kinase B-raf (chains A, B)
GSDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEV
GVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQ
GMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAP
EVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVR
SNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPK

Ligands and cofactors

ID	Name	Formula	Copies
92J	N-{2-methyl-5'-(morpholin-4-yl)-6'-[(oxan-4-yl)oxy][3,3'-bipyridin]-5-yl}-3-(tr…	C28 H29 F3 N4 O4	2

Primary citation

Design and Discovery of N-(2-Methyl-5'-morpholino-6'-((tetrahydro-2H-pyran-4-yl)oxy)-[3,3'-bipyridin]-5-yl)-3-(trifluoromethyl)benzamide (RAF709): A Potent, Selective, and Efficacious RAF Inhibitor Targeting RAS Mutant Cancers. Nishiguchi, G.A., Rico, A., Tanner, H. et al. J Med Chem (2017) 60:4869-4881. DOI 10.1021/acs.jmedchem.6b01862 · 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…

Browse structure collections

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