9FHE

hKHK-C in complex with BI-9787 (pH 5.5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

Starting Model: experimental
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Literature

Discovery of BI-9787, a potent zwitterionic ketohexokinase inhibitor with oral bioavailability.

Heine, N.Weber, A.Pautsch, A.Gottschling, D.Uphues, I.Bauer, M.Ebenhoch, R.Magarkar, A.Nosse, B.Kley, J.T.

(2024) Bioorg Med Chem Lett 112: 129930-129930

  • DOI: https://doi.org/10.1016/j.bmcl.2024.129930
  • Primary Citation of Related Structures:  
    8OMJ, 8OMK, 9FHD, 9FHE

  • PubMed Abstract: 

    Fructose metabolism by ketohexokinase (KHK) is implicated in a variety of metabolic disorders. KHK inhibition is a potential therapeutic strategy for the treatment of diseases including diabetes, non-alcoholic fatty liver disease, and non-alcoholic steatohepatitis. The first small-molecule KHK-inhibitors have entered clinical trials, but it remains unclear if systemic inhibition of KHK by small-molecules will eventually benefit patients. Here we report the discovery of BI-9787, a potent, zwitterionic KHK inhibitor characterized by high permeability and favorable oral rat pharmacokinetics. BI-9787 was identified by optimizing chemical starting points generated via a ligand-based virtual screening of Boehringer's virtual library of synthetically accessible compounds (BICLAIM). It serves as a high-quality in vitro and in vivo tool compound for investigating the role of fructose metabolism in disease.


  • Organizational Affiliation

    Boehringer Ingelheim Pharma GmbH & Co. KG, Global Medicinal Chemistry, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ketohexokinase
A, B
313Homo sapiensMutation(s): 0 
Gene Names: KHK
EC: 2.7.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P50053 (Homo sapiens)
Explore P50053 
Go to UniProtKB:  P50053
PHAROS:  P50053
GTEx:  ENSG00000138030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50053
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ICK (Subject of Investigation/LOI)
Query on A1ICK

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2~{S})-3-[3-[[4-[bis(fluoranyl)methyl]-3-cyano-6-[(3~{S})-3-(dimethylamino)pyrrolidin-1-yl]pyridin-2-yl]amino]-4-methylsulfanyl-phenyl]-2-methyl-propanoic acid
C24 H29 F2 N5 O2 S
LPDOIXPRZOWBJV-HOCLYGCPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.659α = 90
b = 83.123β = 90
c = 146.514γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Cootmodel building
autoPROCdata processing
Aimlessdata scaling

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: 2024-09-04
    Type: Initial release