9FHD | pdb_00009fhd

hKHK-C in fomplex with BI-9787

• PDB DOI: https://doi.org/10.2210/pdb9FHD/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-27 Released: 2024-09-04 
• Deposition Author(s): Ebenhoch, R., Pautsch, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.204 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

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

• PubMed: 39179180 
• DOI: https://doi.org/10.1016/j.bmcl.2024.129930
• Primary Citation 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.

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Organizational Affiliation: 
• Boehringer Ingelheim Pharma GmbH & Co. KG, Global Medicinal Chemistry, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany.
Boehringer Ingelheim Pharma GmbH & Co. KG, Cardiometabolic Diseases Research, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany.
Boehringer Ingelheim Pharma GmbH & Co. KG, Global Medicinal Chemistry, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany; Boehringer Ingelheim International GmbH, Business Development & Licensing, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany.
Boehringer Ingelheim Pharma GmbH & Co. KG, Global Medicinal Chemistry, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 69.42 kDa 
• Atom Count: 5,121 
• Modeled Residue Count: 600 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketohexokinase	A, B	313	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ICK (Subject of Investigation/LOI)	D [auth A], G [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
SO4	C [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.204 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.964	α = 90
b = 86.345	β = 90
c = 136.907	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Coot	model building
Coot	model building
autoPROC	data processing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Ebenhoch, R., Pautsch, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release