6VWC | pdb_00006vwc

Crystal structure of Bcl-xL in complex with tetrahydroisoquinoline-pyridine based inhibitors

• PDB DOI: https://doi.org/10.2210/pdb6VWC/pdb

• Classification: APOPTOSIS/APOPTOSIS INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-02-19 Released: 2020-10-21 
• Deposition Author(s): Judge, R.A., Judd, A.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.200 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.179 (Depositor) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Discovery of A-1331852, a First-in-Class, Potent, and Orally-Bioavailable BCL-X L Inhibitor.

Wang, L., Doherty, G.A., Judd, A.S., Tao, Z.F., Hansen, T.M., Frey, R.R., Song, X., Bruncko, M., Kunzer, A.R., Wang, X., Wendt, M.D., Flygare, J.A., Catron, N.D., Judge, R.A., Park, C.H., Shekhar, S., Phillips, D.C., Nimmer, P., Smith, M.L., Tahir, S.K., Xiao, Y., Xue, J., Zhang, H., Le, P.N., Mitten, M.J., Boghaert, E.R., Gao, W., Kovar, P., Choo, E.F., Diaz, D., Fairbrother, W.J., Elmore, S.W., Sampath, D., Leverson, J.D., Souers, A.J.

(2020) ACS Med Chem Lett 11: 1829-1836

• PubMed: 33062160 
• DOI: https://doi.org/10.1021/acsmedchemlett.9b00568
• Primary Citation Related Structures: 
  6VWC


• PubMed Abstract: 
  

  Herein we describe the discovery of A-1331852, a first-in-class orally active BCL-X _L inhibitor that selectively and potently induces apoptosis in BCL-X _L -dependent tumor cells. This molecule was generated by re-engineering our previously reported BCL-X _L inhibitor A-1155463 using structure-based drug design. Key design elements included rigidification of the A-1155463 pharmacophore and introduction of sp ³ -rich moieties capable of generating highly productive interactions within the key P4 pocket of BCL-X _L . A-1331852 has since been used as a critical tool molecule for further exploring BCL-2 family protein biology, while also representing an attractive entry into a drug discovery program.

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Organizational Affiliation: 
• AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States.
Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.55 kDa 
• Atom Count: 2,610 
• Modeled Residue Count: 278 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 1	A, B	167	Homo sapiens	Mutation(s): 3  Gene Names: BCL2L1, BCL2L, BCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
PHAROS:  Q07817 GTEx:  ENSG00000171552

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RQ7 (Subject of Investigation/LOI)	C [auth A], D [auth B]	6-{8-[(1,3-benzothiazol-2-yl)carbamoyl]-3,4-dihydroisoquinolin-2(1H)-yl}-3-{1-[(pyridin-4-yl)methyl]-1H-pyrazol-4-yl}pyridine-2-carboxylic acid C32 H25 N7 O3 S WBCFKELVKOCTOB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.200 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.179 (Depositor) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.304	α = 90
b = 94.584	β = 90.93
c = 54.272	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-21 
Deposition Author(s): Judge, R.A., Judd, A.S.

Revision History  

• Version 1.0: 2020-10-21
  Type: Initial release
  
• Version 1.1: 2020-11-04
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description