3SPF: Bcl-xL

Crystal Structure of Bcl-xL bound to BM501. Determined by X-ray diffraction at 1.7 Å resolution. Released 27 Jun 2012.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,378
Mol. weight: 20.57 kDa
Ligands: B50
Released: 27 Jun 2012

Explore 3SPF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3SPF contains 9 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: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	2-19	18
α-helix	83-100	18
α-helix	102-111	10
α-helix	119-130	12
α-helix	137-156	20
α-helix	161-173	13
α-helix	174-178	5
α-helix	179-184	6
α-helix	187-195	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bcl-2-like protein 1	A	protein	172	Homo sapiens	Q07817 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3SPF_1 Bcl-2-like protein 1 (chains A)
SEFMSQSNRELVVDFLSYKLSQKGYSWSQFSDVEENRTEAPEGTESEAVKQALREAGDEF
ELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDK
EMQVLVSRIAAWMATYLNDHLEPWIQENGGWDTFVELYGNNAAAESRKGQER

Ligands and cofactors

ID	Name	Formula	Copies
B50	4-(4-chlorophenyl)-1-[(3S)-3,4-dihydroxybutyl]-N-[3-(4-methylpiperazin-1-yl)pro…	C29 H37 Cl N4 O3	1

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

Primary citation

Design of Bcl-2 and Bcl-xL Inhibitors with Subnanomolar Binding Affinities Based upon a New Scaffold. Zhou, H., Chen, J., Meagher, J.L. et al. J Med Chem (2012) 55:4664-4682. DOI 10.1021/jm300178u · PubMed

Other PDB entries of the same protein (UniProt Q07817 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7JGW 1.3 Å, Crystal structure of BCL-XL in complex with COMPOUND 1620116, CRYSTAL FORM 1
3SP7 1.4 Å, Crystal Structure of Bcl-xL bound to BM903
7YAA 1.4 Å, Crystal structure analysis of cp3 bound BCLxl
7LH7 1.41 Å, Crystal structure of BCL-XL in complex with a benzothiazole-based inhibitor
9IGG 1.5 Å, Structure of human Bcl-xL in complex with small molecule inhibitor
4QVF 1.53 Å, Crystal structure of Bcl-xL in complex with BIM BH3 domain
4A1U 1.54 Å, Crystal structure of alpha-beta-foldamer 2c in complex with Bcl-xL
6VWC 1.6 Å, Crystal structure of Bcl-xL in complex with tetrahydroisoquinoline-pyridine based…
6O0K 1.62 Å, crystal structure of BCL-2 with venetoclax
9I9E 1.7 Å, Structure of human Bcl-xL in complex with small molecule inhibitor
9O14 1.73 Å, Crystal Structure of BCL-2 in complex with a stapled BAD BH3 peptide BAD SAHB 4.2
9O16 1.73 Å, Crystal Structure of human BCL-2 (R129L) mutant in complex with a stapled BAD BH3…

Browse structure collections

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