3SP7: Bcl-xL

Crystal Structure of Bcl-xL bound to BM903. Determined by X-ray diffraction at 1.4 Å resolution. Released 4 Jul 2012.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,525
Mol. weight: 21.02 kDa
Ligands: 03B, ZN
Released: 4 Jul 2012

Explore 3SP7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3SP7 contains 11 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: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	3-18	16
α-helix	24-26	3
α-helix	83-101	19
α-helix	102-104	3
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	188-198	11

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

>3SP7_1 Bcl-2-like protein 1 (chains A)
SEFMSQSNRELVVDFLSYKLSQKGYSWSQFSDVEENRTEAPEGTESEAVKQALREAGDEF
ELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDK
EMQVLVSRIAAWMATYLNDHLEPWIQENGGWDTFVELYGNNAAAESRKGQER

Ligands and cofactors

ID	Name	Formula	Copies
03B	5-(4-chlorophenyl)-4-{3-[4-(4-{[(4-{[(2R)-4-(dimethylamino)-1-(phenylsulfanyl)b…	C47 H50 Cl N7 O6 S2	1
ZN	Zinc ion	Zn	4

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

Primary citation

Structure-based design of a new class of potent Bcl-2/Bcl-xL inhibitors. Zhou, H., Chen, J., Meagher, J.L. et al. To be published.

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
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
3SPF 1.7 Å, Crystal Structure of Bcl-xL bound to BM501
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…

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