7LHB | pdb_00007lhb

Crystal structure of Bcl-2 in complex with prodrug ABBV-167


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 
    0.238 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Expanding the Repertoire for "Large Small Molecules": Prodrug ABBV-167 Efficiently Converts to Venetoclax with Reduced Food Effect in Healthy Volunteers.

Salem, A.H.Tao, Z.F.Bueno, O.F.Chen, J.Chen, S.Edalji, R.Elmore, S.W.Fournier, K.M.Harper, K.C.Hong, R.Jenkins, G.J.Ji, J.Judge, R.A.Kalvass, J.C.Klix, R.C.Ku, Y.Y.Leverson, J.D.Marks, R.A.Marsh, K.C.Menon, R.M.Park, C.H.Phillips, D.C.Pu, Y.M.Rosenberg, S.H.Sanzgiri, Y.D.Sheikh, A.Y.Shi, Y.Stolarik, D.Suleiman, A.A.Wang, X.Zhang, G.G.Z.Catron, N.D.Souers, A.J.

(2021) Mol Cancer Ther 20: 999-1008

  • DOI: https://doi.org/10.1158/1535-7163.MCT-21-0077
  • Primary Citation Related Structures: 
    7LHB

  • PubMed Abstract: 

    Since gaining approval for the treatment of chronic lymphocytic leukemia (CLL), the BCL-2 inhibitor venetoclax has transformed the treatment of this and other blood-related cancers. Reflecting the large and hydrophobic BH3-binding groove within BCL-2, venetoclax has significantly higher molecular weight and lipophilicity than most orally administered drugs, along with negligible water solubility. Although a technology-enabled formulation successfully achieves oral absorption in humans, venetoclax tablets have limited drug loading and therefore can present a substantial pill burden for patients in high-dose indications. We therefore generated a phosphate prodrug ( 3 , ABBV-167) that confers significantly increased water solubility to venetoclax and, upon oral administration to healthy volunteers either as a solution or high drug-load immediate release tablet, extensively converts to the parent drug. Additionally, ABBV-167 demonstrated a lower food effect with respect to venetoclax tablets. These data indicate that beyond-rule-of-5 molecules can be successfully delivered to humans via a solubility-enhancing prodrug moiety to afford robust exposures of the parent drug following oral dosing.


  • Organizational Affiliation
    • AbbVie, Inc., North Chicago, Illinois.

Macromolecule Content 

  • Total Structure Weight: 61 kDa 
  • Atom Count: 3,789 
  • Modeled Residue Count: 403 
  • Deposited Residue Count: 498 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Apoptosis regulator Bcl-2
A, B, C
166Homo sapienssynthetic constructMutation(s): 2 
Gene Names: BCL2
UniProt & NIH Common Fund Data Resources
Find proteins for P10415 (Homo sapiens)
Explore P10415 
Go to UniProtKB:  P10415
PHAROS:  P10415
GTEx:  ENSG00000171791 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10415
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XZD
(Subject of Investigation/LOI)

Query on XZD



Download:Ideal Coordinates CCD File
D [auth A],
E [auth B],
F [auth C]
Phosphoric acid mono-[5-(5-{4-[2-(4-chloro-phenyl)-4,4-dimethyl-cyclohex-1-enylmethyl]-piperazin-1-yl}-2-{3-nitro-4-[(tetrahydro-pyran-4-ylmethyl)-amino]-benzenesulfonylaminocarbonyl}-phenoxy)-pyrrolo[2,3-b]pyridin-7-ylmethyl] ester
C46 H53 Cl N7 O11 P S
CLQLTQZFOGFNCT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.362α = 90
b = 49.448β = 103.63
c = 89.359γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 2.0: 2022-04-13
    Changes: Database references, Non-polymer description, Structure summary
  • Version 2.1: 2023-10-18
    Changes: Data collection, Refinement description