9FKZ: Bcl-2-related protein A1

Discovery of a Series of Covalent, Cell Active Bfl-1 Inhibitors. Determined by X-ray diffraction at 1.68 Å resolution. Released 2 Oct 2024.

Method: X-ray diffraction
Resolution: 1.68 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,286
Mol. weight: 17.81 kDa
Ligands: A1IDO
Released: 2 Oct 2024

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

Secondary structure: helices and β-sheets

9FKZ contains 10 α-helices and 0 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: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	6-21	16
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	112-114	3
α-helix	115-136	22
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	protein	152	Homo sapiens	Q16548 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9FKZ_1 Bcl-2-related protein A1 (chains A)
GMTDCEFGYIYRLAQDYLQCVLQIPQPGSGPSKTSRVLQNVAFSVQKEVEKNLKSCLDNV
NVVSVDTARTLFNQVMEKEFEDGIINWGRIVTIFAFEGILIKKLLRQQIAPDVDTYKEIS
YFVAEFIMNNTGEWIRQNGGWENGFVKKFEPK

Ligands and cofactors

ID	Name	Formula	Copies
A1IDO	~{N}-[4-[(1~{R},3~{R})-3-azanylcyclopentyl]oxyphenyl]-~{N}-[(4-chlorophenyl)met…	C21 H23 Cl N2 O2	1

Primary citation

Structure-Based Optimization of a Series of Covalent, Cell Active Bfl-1 Inhibitors. Lucas, S.C.C., Blackwell, J.H., Borjesson, U. et al. J Med Chem (2024) 67:16455-16479. DOI 10.1021/acs.jmedchem.4c01288 · 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
9S6M 1.43 Å, Structure of BFL1 in complex with a covalent inhibitor, alternative series, cmpd25
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

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