1YSI | pdb_00001ysi

Solution structure of the anti-apoptotic protein Bcl-xL in complex with an acyl-sulfonamide-based ligand


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

Literature

An inhibitor of Bcl-2 family proteins induces regression of solid tumours

Oltersdorf, T.Elmore, S.W.Shoemaker, A.R.Armstrong, R.C.Augeri, D.J.Belli, B.A.Bruncko, M.Deckwerth, T.L.Dinges, J.Hajduk, P.J.Joseph, M.K.Kitada, S.Korsmeyer, S.J.Kunzer, A.R.Letai, A.Li, C.Mitten, M.J.Nettesheim, D.G.Ng, S.Nimmer, P.M.O'Connor, J.M.Oleksijew, A.Petros, A.M.Reed, J.C.Shen, W.Tahir, S.K.Thompson, C.B.Tomaselli, K.J.Wang, B.Wendt, M.D.Zhang, H.Fesik, S.W.Rosenberg, S.H.

(2005) Nature 435: 677-681

  • DOI: https://doi.org/10.1038/nature03579
  • Primary Citation Related Structures: 
    1YSG, 1YSI, 1YSN, 1YSW, 1YSX

  • PubMed Abstract: 

    Proteins in the Bcl-2 family are central regulators of programmed cell death, and members that inhibit apoptosis, such as Bcl-X(L) and Bcl-2, are overexpressed in many cancers and contribute to tumour initiation, progression and resistance to therapy. Bcl-X(L) expression correlates with chemo-resistance of tumour cell lines, and reductions in Bcl-2 increase sensitivity to anticancer drugs and enhance in vivo survival. The development of inhibitors of these proteins as potential anti-cancer therapeutics has been previously explored, but obtaining potent small-molecule inhibitors has proved difficult owing to the necessity of targeting a protein-protein interaction. Here, using nuclear magnetic resonance (NMR)-based screening, parallel synthesis and structure-based design, we have discovered ABT-737, a small-molecule inhibitor of the anti-apoptotic proteins Bcl-2, Bcl-X(L) and Bcl-w, with an affinity two to three orders of magnitude more potent than previously reported compounds. Mechanistic studies reveal that ABT-737 does not directly initiate the apoptotic process, but enhances the effects of death signals, displaying synergistic cytotoxicity with chemotherapeutics and radiation. ABT-737 exhibits single-agent-mechanism-based killing of cells from lymphoma and small-cell lung carcinoma lines, as well as primary patient-derived cells, and in animal models, ABT-737 improves survival, causes regression of established tumours, and produces cures in a high percentage of the mice.


  • Organizational Affiliation
    • Idun Pharmaceuticals, 9380 Judicial Drive, San Diego, California 92121, USA.

Macromolecule Content 

  • Total Structure Weight: 21.36 kDa 
  • Atom Count: 1,505 
  • Modeled Residue Count: 181 
  • Deposited Residue Count: 181 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Apoptosis regulator Bcl-X181Homo sapiensMutation(s): 0 
Gene Names: BCL2L1BCL2LBCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
PHAROS:  Q07817
GTEx:  ENSG00000171552 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07817
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N3B

Query on N3B



Download:Ideal Coordinates CCD File
B [auth A]N-[(4'-FLUORO-1,1'-BIPHENYL-4-YL)CARBONYL]-3-NITRO-4-{[2-(PHENYLSULFANYL)ETHYL]AMINO}BENZENESULFONAMIDE
C27 H22 F N3 O5 S2
SWGIDRBGIJDBQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-07
    Type: Initial release
  • Version 1.1: 2007-10-17
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2022-03-02
    Changes: Atomic model, Database references, Derived calculations
  • Version 2.1: 2024-05-22
    Changes: Data collection