Ornithine Aminotransferase (OAT) cocrystallized with its potent inhibitor - (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148)

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

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Turnover and Inactivation Mechanisms for ( S )-3-Amino-4,4-difluorocyclopent-1-enecarboxylic Acid, a Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase.

Shen, S.Butrin, A.Doubleday, P.F.Melani, R.D.Beaupre, B.A.Tavares, M.T.Ferreira, G.M.Kelleher, N.L.Moran, G.R.Liu, D.Silverman, R.B.

(2021) J Am Chem Soc 143: 8689-8703

  • DOI: https://doi.org/10.1021/jacs.1c02456
  • Primary Citation of Related Structures:  
    7LK0, 7LK1

  • PubMed Abstract: 

    The inhibition of human ornithine δ-aminotransferase ( h OAT) is a potential therapeutic approach to treat hepatocellular carcinoma. In this work, ( S )-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148, 6 ) was identified as a potent mechanism-based inactivator of h OAT while showing excellent selectivity over other related aminotransferases (e.g., GABA-AT). An integrated mechanistic study was performed to investigate the turnover and inactivation mechanisms of 6 . A monofluorinated ketone ( M10 ) was identified as the primary metabolite of 6 in h OAT. By soaking h OAT holoenzyme crystals with 6 , a precursor to M10 was successfully captured. This gem -diamine intermediate, covalently bound to Lys292, observed for the first time in h OAT/ligand crystals, validates the turnover mechanism proposed for 6 . Co-crystallization yielded h OAT in complex with 6 and revealed a novel noncovalent inactivation mechanism in h OAT. Native protein mass spectrometry was utilized for the first time in a study of an aminotransferase inactivator to validate the noncovalent interactions between the ligand and the enzyme; a covalently bonded complex was also identified as a minor form observed in the denaturing intact protein mass spectrum. Spectral and stopped-flow kinetic experiments supported a lysine-assisted E2 fluoride ion elimination, which has never been observed experimentally in other studies of related aminotransferase inactivators. This elimination generated the second external aldimine directly from the initial external aldimine, rather than the typical E1cB elimination mechanism, forming a quinonoid transient state between the two external aldimines. The use of native protein mass spectrometry, X-ray crystallography employing both soaking and co-crystallization methods, and stopped-flow kinetics allowed for the detailed elucidation of unusual turnover and inactivation pathways.

  • Organizational Affiliation

    Department of Chemistry, 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, mitochondrial
A, B, C
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y3D (Subject of Investigation/LOI)
Query on Y3D

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
(1R,3S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxocyclopentane-1-carboxylic acid
C14 H17 N2 O8 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.707α = 90
b = 192.707β = 90
c = 56.804γ = 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: 2022-02-16
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description