Human Ornithine Aminotransferase cocrystallized with its inhibitor, (S,E)-3-amino-4-(fluoromethylene)cyclopent-1-ene-1-carboxylate

Experimental Data Snapshot

  • Resolution: 2.63 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 

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Rational Design, Synthesis, and Mechanism of (3 S ,4 R )-3-Amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylic Acid: Employing a Second-Deprotonation Strategy for Selectivity of Human Ornithine Aminotransferase over GABA Aminotransferase.

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

(2022) J Am Chem Soc 144: 5629-5642

  • DOI: https://doi.org/10.1021/jacs.2c00924
  • Primary Citation of Related Structures:  
    7TED, 7TEV, 7TFP

  • PubMed Abstract: 

    Human ornithine aminotransferase (hOAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that contains a similar active site to that of γ-aminobutyric acid aminotransferase (GABA-AT). Recently, pharmacological inhibition of hOAT was recognized as a potential therapeutic approach for hepatocellular carcinoma. In this work, we first studied the inactivation mechanisms of hOAT by two well-known GABA-AT inactivators ( CPP-115 and OV329 ). Inspired by the inactivation mechanistic difference between these two aminotransferases, a series of analogues were designed and synthesized, leading to the discovery of analogue 10b as a highly selective and potent hOAT inhibitor. Intact protein mass spectrometry, protein crystallography, and dialysis experiments indicated that 10b was converted to an irreversible tight-binding adduct ( 34 ) in the active site of hOAT, as was the unsaturated analogue ( 11 ). The comparison of kinetic studies between 10b and 11 suggested that the active intermediate ( 17b ) was only generated in hOAT and not in GABA-AT. Molecular docking studies and p K a computational calculations highlighted the importance of chirality and the endocyclic double bond for inhibitory activity. The turnover mechanism of 10b was supported by mass spectrometric analysis of dissociable products and fluoride ion release experiments. Notably, the stopped-flow experiments were highly consistent with the proposed mechanism, suggesting a relatively slow hydrolysis rate for hOAT. The novel second-deprotonation mechanism of 10b contributes to its high potency and significantly enhanced selectivity for hOAT inhibition.

  • Organizational Affiliation

    Department of Chemistry, Chemistry of Life Processes Institute, 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, D, E
A, B, C, D, E, F, G, H, I
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I1T (Subject of Investigation/LOI)
Query on I1T

Download Ideal Coordinates CCD File 
J [auth A]
K [auth B]
L [auth C]
M [auth D]
N [auth E]
J [auth A],
K [auth B],
L [auth C],
M [auth D],
N [auth E],
O [auth F],
P [auth G],
Q [auth H]
(1S,3R,4S)-3-formyl-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopentane-1-carboxylic acid
C15 H21 N2 O8 P
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
C8 H10 N O6 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.63 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.11α = 90
b = 115.43β = 94.85
c = 185.76γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

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 States1R01CA260250-01
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01DA030604

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description