8V9M

Human Ornithine Aminotransferase cocrystallized with its inhibitor, (R)-3-amino-5,5-difluorocyclohex-1-ene-1-carboxylic acid.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

Starting Model: experimental
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Literature

Design, Synthesis, and Mechanistic Studies of ( R )-3-Amino-5,5-difluorocyclohex-1-ene-1-carboxylic Acid as an Inactivator of Human Ornithine Aminotransferase.

Devitt, A.N.Vargas, A.L.Zhu, W.Des Soye, B.J.Butun, F.A.Alt, T.Kaley, N.Ferreira, G.M.Moran, G.R.Kelleher, N.L.Liu, D.Silverman, R.B.

(2024) ACS Chem Biol 19: 1066-1081

  • DOI: https://doi.org/10.1021/acschembio.4c00022
  • Primary Citation of Related Structures:  
    8V9M

  • PubMed Abstract: 

    Human ornithine aminotransferase ( h OAT), a pyridoxal 5'-phosphate (PLP)-dependent enzyme, has been shown to play an essential role in the metabolic reprogramming and progression of hepatocellular carcinoma (HCC). HCC accounts for approximately 75% of primary liver cancers and is within the top three causes of cancer death worldwide. As a result of treatment limitations, the overall 5-year survival rate for all patients with HCC is under 20%. The prevalence of HCC necessitates continued development of novel and effective treatment methods. In recent years, the therapeutic potential of selective inactivation of h OAT has been demonstrated for the treatment of HCC. Inspired by previous increased selectivity for h OAT by the expansion of the cyclopentene ring scaffold to a cyclohexene, we designed, synthesized, and evaluated a series of novel fluorinated cyclohexene analogues and identified (R)-3-amino-5,5-difluorocyclohex-1-ene-1-carboxylic acid as a time-dependent inhibitor of h OAT. Structural and mechanistic studies have elucidated the mechanism of inactivation of h OAT by 5 , resulting in a PLP-inactivator adduct tightly bound to the active site of the enzyme. Intact protein mass spectrometry, 19 F NMR spectroscopy, transient state kinetic studies, and X-ray crystallography were used to determine the structure of the final adduct and elucidate the mechanisms of inactivation. Interestingly, despite the highly electrophilic intermediate species conferred by fluorine and structural evidence of solvent accessibility in the h OAT active site, Lys292 and water did not participate in nucleophilic addition during the inactivation mechanism of h OAT by 5 . Instead, rapid aromatization to yield the final adduct was favored.


  • Organizational Affiliation

    Department of Chemistry, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ornithine aminotransferase, mitochondrial
A, B, C
404Homo sapiensMutation(s): 0 
Gene Names: OAT
EC: 2.6.1.13
UniProt & NIH Common Fund Data Resources
Find proteins for P04181 (Homo sapiens)
Explore P04181 
Go to UniProtKB:  P04181
PHAROS:  P04181
GTEx:  ENSG00000065154 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04181
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.334α = 90
b = 115.334β = 90
c = 186.292γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA260250

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references