9AQZ

Crystal structure of Bcl-xL in complex with a small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

BCL-X L -targeting antibody-drug conjugates are active in preclinical models and mitigate on-mechanism toxicity of small-molecule inhibitors.

Judd, A.S.Bawa, B.Buck, W.R.Tao, Z.F.Li, Y.Mitten, M.J.Bruncko, M.Catron, N.Doherty, G.Durbin, K.R.Enright, B.Frey, R.Haasch, D.Haman, S.Haight, A.R.Henriques, T.A.Holms, J.Izeradjene, K.Judge, R.A.Jenkins, G.J.Kunzer, A.Leverson, J.D.Martin, R.L.Mitra, D.Mittelstadt, S.Nelson, L.Nimmer, P.Palma, J.Peterson, R.Phillips, D.C.Ralston, S.L.Rosenberg, S.H.Shen, X.Song, X.Vaidya, K.R.Wang, X.Wang, J.Xiao, Y.Zhang, H.Zhang, X.Blomme, E.A.Boghaert, E.R.Kalvass, J.C.Phillips, A.Souers, A.J.

(2024) Sci Adv 10: eado7120-eado7120

  • DOI: https://doi.org/10.1126/sciadv.ado7120
  • Primary Citation of Related Structures:  
    9AQZ

  • PubMed Abstract: 

    Overexpression of the antiapoptotic protein B-cell lymphoma-extra large (BCL-X L ) is associated with drug resistance and disease progression in numerous cancers. The compelling nature of this protein as a therapeutic target prompted efforts to develop selective small-molecule BCL-X L inhibitors. Although efficacious in preclinical models, we report herein that selective BCL-X L inhibitors cause severe mechanism-based cardiovascular toxicity in higher preclinical species. To overcome this liability, antibody-drug conjugates were constructed using altered BCL-X L -targeting warheads, unique linker technologies, and therapeutic antibodies. The epidermal growth factor receptor-targeting antibody-drug conjugate AM1-15 inhibited growth of tumor xenografts and did not cause cardiovascular toxicity nor dose-limiting thrombocytopenia in monkeys. While an unprecedented BCL-X L -mediated toxicity was uncovered in monkey kidneys upon repeat dosing of AM1-15, this toxicity was mitigated via further drug-linker modification to afford AM1-AAA (AM1-25). The AAA drug-linker has since been incorporated into mirzotamab clezutoclax, the first selective BCL-X L -targeting agent to enter human clinical trials.


  • Organizational Affiliation

    AbbVie Inc., 1 N. Waukegan Road, North Chicago, IL 60064, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bcl-2-like protein 1167Homo sapiensMutation(s): 3 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AFG (Subject of Investigation/LOI)
Query on A1AFG

Download Ideal Coordinates CCD File 
B [auth A](3M)-3-(1-{[(1r,3R,5S,7r)-adamantan-1-yl]methyl}-5-methyl-1H-pyrazol-4-yl)-6-{8-[(1,3-benzothiazol-2-yl)carbamoyl]-3,4-dihydroisoquinolin-2(1H)-yl}pyridine-2-carboxylic acid
C38 H38 N6 O3 S
QCQQONWEDCOTBV-XBSKGOHMSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.031α = 90
b = 78.389β = 90
c = 144.774γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Database references