Ornithine Aminotransferase (OAT) cocrystallized with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclohexene-1-carboxylic acid

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

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Remarkable and Unexpected Mechanism for ( S )-3-Amino-4-(difluoromethylenyl)cyclohex-1-ene-1-carboxylic Acid as a Selective Inactivator of Human Ornithine Aminotransferase.

Zhu, W.Doubleday, P.F.Butrin, A.Weerawarna, P.M.Melani, R.D.Catlin, D.S.Dwight, T.A.Liu, D.Kelleher, N.L.Silverman, R.B.

(2021) J Am Chem Soc 143: 8193-8207

  • DOI: https://doi.org/10.1021/jacs.1c03572
  • Primary Citation of Related Structures:  
    7LNM, 7LOM, 7LON

  • PubMed Abstract: 

    Human ornithine aminotransferase ( h OAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that was recently found to play an important role in the metabolic reprogramming of hepatocellular carcinoma (HCC) via the proline and glutamine metabolic pathways. The selective inhibition of h OAT by compound 10 exhibited potent in vivo antitumor activity. Inspired by the discovery of the aminotransferase inactivator (1 S ,3 S )-3-amino-4-(difluoromethylene)cyclopentane-1-carboxylic acid ( 5 ), we rationally designed, synthesized, and evaluated a series of six-membered-ring analogs. Among them, 14 was identified as a new selective h OAT inactivator, which demonstrated a potency 22× greater than that of 10 . Three different types of protein mass spectrometry approaches and two crystallographic approaches were employed to identify the structure of h OAT- 14 and the formation of a remarkable final adduct ( 32' ) in the active site. These spectral studies reveal an enzyme complex heretofore not observed in a PLP-dependent enzyme, which has covalent bonds to two nearby residues. Crystal soaking experiments and molecular dynamics simulations were carried out to identify the structure of the active-site intermediate 27' and elucidate the order of the two covalent bonds that formed, leading to 32' . The initial covalent reaction of the activated warhead occurs with *Thr322 from the second subunit, followed by a subsequent nucleophilic attack by the catalytic residue Lys292. The turnover mechanism of 14 by h OAT was supported by a mass spectrometric analysis of metabolites and fluoride ion release experiments. This novel mechanism for h OAT with 14 will contribute to the further rational design of selective inactivators and an understanding of potential inactivation mechanisms by aminotransferases.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ornithine aminotransferase, mitochondrialA [auth B],
B [auth A],
404Homo sapiensMutation(s): 0 
Gene Names: OAT
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.024α = 90
b = 192.024β = 90
c = 57.058γ = 120
Software Package:
Software NamePurpose
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description