9S6M: BFL1

Structure of BFL1 in complex with a covalent inhibitor, alternative series, cmpd25. Determined by X-ray diffraction at 1.43 Å resolution. Released 14 Jan 2026.

Method: X-ray diffraction
Resolution: 1.43 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,601
Mol. weight: 35.81 kDa
Ligands: A1JL2
Released: 14 Jan 2026

Explore 9S6M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9S6M contains 24 α-helices and 0 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: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	6-20	15
α-helix	24-25	2
α-helix	32-51	20
α-helix	53-56	4
α-helix	64-78	15
α-helix	86-106	21
α-helix	114-125	12
α-helix	126-130	5
α-helix	131-136	6
α-helix	139	1
α-helix	140-144	5
α-helix	145-148	4

Chain B: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	6-20	15
α-helix	32-51	20
α-helix	53-56	4
α-helix	64-78	15
α-helix	86-106	21
α-helix	112-114	3
α-helix	115-125	11
α-helix	126-130	5
α-helix	131-136	6
α-helix	139	1
α-helix	140-144	5
α-helix	145-148	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bcl-2-related protein A1	A, B	protein	152	Homo sapiens	Q16548 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9S6M_1 Bcl-2-related protein A1 (chains A, B)
GMTDCEFGYIYRLAQDYLQCVLQIPQPGSGPSKTSRVLQNVAFSVQKEVEKNLKSCLDNV
NVVSVDTARTLFNQVMEKEFEDGIINWGRIVTIFAFEGILIKKLLRQQIAPDVDTYKEIS
YFVAEFIMNNTGEWIRQNGGWENGFVKKFEPK

Ligands and cofactors

ID	Name	Formula	Copies
A1JL2	(1~{R},2~{R})-2-azanyl-~{N}-[4-[(1~{R})-1-[propanoyl-[4-(trifluoromethyloxy)phe…	C24 H28 F3 N3 O3	2

Primary citation

Optimization and Chemoproteomic Profiling of a Selective, Covalent Bfl-1-Targeting Cellular Tool. Blackwell, J.H., Lucas, S.C.C., Battocchio, G. et al. J Med Chem (2026) 69:1218-1246. DOI 10.1021/acs.jmedchem.5c02581 · PubMed

Other PDB entries of the same protein (UniProt Q16548 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GIR 1.07 Å, BFL1 covalently bound to inhibitor compound 39
9GIT 1.15 Å, BFL1 covalently bound to inhibitor compound 43
5UUK 1.2 Å, Human Bfl-1 in complex with a Bfl-1-specific selected peptide
5UUL 1.33 Å, Human Bfl-1 in complex with PUMA BH3
9GIS 1.39 Å, BFL1 covalently bound to inhibitor compound 17
9GIQ 1.42 Å, BFL1 covalently bound to inhibitor compound 13
9GIP 1.46 Å, BFL1 covalently bound to inhibitor compound 7
6E3I 1.48 Å, Human Bfl-1 in complex with the Bfl-1-specific designed peptide srt.F4
6E3J 1.48 Å, Human Bfl-1 in complex with the Bfl-1-specific designed peptide srt.F10
9EW8 1.49 Å, Discovery of a Series of Covalent, Cell Active Bfl-1 Inhibitors
9FKY 1.56 Å, Discovery of a Series of Covalent, Cell Active Bfl-1 Inhibitors
6MBB 1.59 Å, Human Bfl-1 in complex with the designed peptide dF1

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