9Y3K

Crystal Structure of Human Ornithine Aminotransferase Pre-Inactivated by CPP115 (Tight Binding)

Summary for 9Y3K

• Entry DOI: 10.2210/pdb9y3k/pdb
• Descriptor: Ornithine aminotransferase, mitochondrial, (1S)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-3-ene-1,3-dicarboxylic acid (3 entities in total)
• Functional Keywords: mechanism based inactivator, aminotransferase, transferase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 3
• Total formula weight: 135787.84

Authors

Corrigan, M.C.,Vargas, A.L.,Kang, K.M.,Silverman, R.B.,Liu, D. (deposition date: 2025-09-02, release date: 2026-07-22)

Primary citation

Kang, K.M.,Vargas, A.L.,Ferreira, L.A.,Des Soye, B.J.,Corrigan, M.,Zhang, C.K.,Wang, F.,Duan, D.,Kelleher, N.L.,Hohmann, A.G.,Liu, D.,Silverman, R.B.
Targeting Conformational Flexibility of a Reactive Intermediate to Enhance Selectivity of a GABA Aminotransferase Inactivator.
J.Am.Chem.Soc., 148:8736-8748, 2026

PubMed Abstract: Currently, mechanism-based inactivators (MBIs) are the only available therapeutic option to target γ-aminobutyric acid aminotransferase (GABA-AT). However, off-target activity against homologous enzymes is a well-recognized challenge for the clinical use of MBIs. For example, CPP-115, an MBI of GABA-AT that completed a Phase I clinical trial, also inactivates ornithine aminotransferase (OAT). Here, we present a comprehensive investigation of an OAT-specific inactivation mechanism for CPP-115 by integrating biochemical experiments, X-ray crystallography, and computational simulations. Unlike in GABA-AT, where CPP-115 forms a noncovalent tight-binding adduct only, a covalent adduct was additionally observed with human OAT (OAT). Notably, the crystal structures of CPP-115-treated OAT at different mechanistic stages indicate that the conformational transition of a key intermediate is a prerequisite for the covalent addition pathway. Based on this finding, to selectively reduce the off-target activity, a proof-of-concept molecule that regulates the intermediate conformational flexibility was designed and synthesized. The resulting inactivator achieved greatly enhanced GABA-AT selectivity over OAT and demonstrated therapeutic efficacy in an inflammatory pain animal model. Our strategy in this study, targeting dynamics of a reactive intermediate based on a precise mechanistic understanding, serves as a general design principle for fine-tuning the selectivity of MBIs, particularly for other aminotransferases.

PubMed: 41711325
DOI: 10.1021/jacs.5c21138

Experimental method

X-RAY DIFFRACTION (2.15 Å)