9I9E: Human Bcl-xL

Structure of human Bcl-xL in complex with small molecule inhibitor. Determined by X-ray diffraction at 1.7 Å resolution. Released 24 Jun 2026.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,024
Mol. weight: 74.49 kDa
Ligands: A1I1S
Released: 24 Jun 2026

Explore 9I9E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I9E contains 40 α-helices and 0 β-strands across 4 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: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	2-20	19
α-helix	25-27	3
α-helix	41-104	24
α-helix	108-111	4
α-helix	120-131	12
α-helix	137-156	20
α-helix	162-177	16
α-helix	179-184	6
α-helix	187-195	9

Chain B: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	2-18	17
α-helix	25-27	3
α-helix	31-33	3
α-helix	42-104	23
α-helix	108-111	4
α-helix	120-130	11
α-helix	137-156	20
α-helix	162-173	12
α-helix	174-178	5
α-helix	179-184	6
α-helix	187-195	9

Chain C: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	5-18	14
α-helix	42-104	23
α-helix	108-111	4
α-helix	120-130	11
α-helix	137-156	20
α-helix	162-173	12
α-helix	174-178	5
α-helix	179-184	6
α-helix	188-195	8

Chain D: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	5-19	15
α-helix	25-27	3
α-helix	42-104	23
α-helix	108-111	4
α-helix	120-128	9
α-helix	129-131	3
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
Apoptosis regulator Bcl-2,Bcl-2-like protein 1	A, B, C, D	protein	159	Homo sapiens	P10415 (AlphaFold model), Q07817 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9I9E_1 Apoptosis regulator Bcl-2,Bcl-2-like protein 1 (chains A, B, C, D)
GSYDNREIVMKYIHYKLSQRGYEWDAGADVEENRTEAPEGTESEVVKQALREAGDEFELR
YRRAFSDLTSQLHLTPGTAYGSFATVVNELFRDGVNWGRIVAFFSFGGALCVESVNREMS
PLVDNIALWMTEYLNRHLHTWIQDNGGWDAFVELYGPSM

Ligands and cofactors

ID	Name	Formula	Copies
A1I1S	2-[(8~{E})-8-(1,3-benzothiazol-2-ylhydrazinylidene)-6,7-dihydro-5~{H}-naphthale…	C21 H16 N4 O2 S2	4

Primary citation

Structure-Based Discovery of Potent BCL-XL Inhibitors through Rescaffolding. Timari, M.P., Paczal, A., Herner, A. et al. J Med Chem (2026) 69:14804-14818. DOI 10.1021/acs.jmedchem.6c00865 · PubMed

Other PDB entries of the same protein (UniProt P10415 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8HTS 1.25 Å, Crystal structure of Bcl2 in complex with S-10r
6GL8 1.4 Å, Crystal structure of Bcl-2 in complex with the novel orally active inhibitor S55746
6QGG 1.5 Å, Structure of human Bcl-2 in complex with analogue of ABT-737
9IGG 1.5 Å, Structure of human Bcl-xL in complex with small molecule inhibitor
8HTR 1.6 Å, Crystal structure of Bcl2 in complex with S-9c
6O0K 1.62 Å, crystal structure of BCL-2 with venetoclax
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…
6O0M 1.75 Å, crystal structure of BCL-2 F104L mutation with venetoclax
5VAU 1.75 Å, Bcl-2 complex with Beclin 1 BH3 domain
8VWX 1.77 Å, Human Bcl-2 (G101V Mutant)/Bcl-xL Chimera Fused to Maltose-Binding Protein
6O0P 1.8 Å, crystal structure of BCL-2 G101A mutation with venetoclax

Browse structure collections

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