American Society of Hirudotherapy

Crystal structure of human alpha-thrombin complexed with hirugen and p-amidinophenylpyruvate at 1.6 A resolution

Research article published in Archives of biochemistry and biophysics (1995)

Last Updated: June 18, 2026Reviewed by: ASH Editorial Board
Research article — evidence reviewArticle reference
Evidence: Research reportDrug DevelopmentChen Z et al. · Archives of biochemistry and biophysics, 1995

Abstract

Crystals of human alpha-thrombin complexed with hirugen and the alpha-keto acid thrombin inhibitor APPA (p-amidinophenylpyruvate) that diffract to 1.6 A resolution were obtained by soaking an alpha-thrombin-hirugen crystal in a solution of APPA. The crystal structure was determined using the difference Fourier method and refined to an R factor of 18.7% at 1.6 A resolution. This structure is the highest resolution structure of the thrombin molecule that is currently available. With the exception of the region near Arg77A-Asn78, the structures of the thrombin and hirugen molecules in the ternary complex are similar to those reported for the thrombin-hirugen binary complex. As previously determined for the APPA-trypsin complex, the carbonyl carbon atom of APPA forms a covalent bond with O gamma of Ser195 of thrombin to yield a "transition-state" analog of the tetrahedral intermediate. Comparison of the specificity pocket of the APPA complexes of thrombin and trypsin reveals differences in hydrogen bonding and shows for the first time that the S1 site of thrombin is larger than that of trypsin and as a result thrombin may be able to accommodate a bulkier P1 group than trypsin.

Abstract sourced from PubMed (NCBI) for the cited record. See the original publication for the authoritative version.

Publication typeJournal Article
Indexed MeSH termsAmino Acid SequenceBinding SitesCrystallizationCrystallography, X-RayHirudinsHumansHydrogen BondingIn Vitro TechniquesModels, MolecularMolecular Sequence DataMolecular StructurePeptide Fragments

Summary

Crystals of human alpha-thrombin complexed with hirugen and the alpha-keto acid thrombin inhibitor APPA (p-amidinophenylpyruvate) that diffract to 1.6 A resolution were obtained by soaking an alpha-thrombin-hirugen crystal in a solution of APPA.

Why This Matters for Hirudotherapy

This article describes the 1.6 Å resolution crystal structure of human alpha-thrombin complexed with hirugen and APPA (p-amidinophenylpyruvate), reported as the highest resolution thrombin structure currently available. The abstract states that the thrombin and hirugen molecules in the ternary complex are similar to those reported for the thrombin-hirugen binary complex, describes the covalent bond between APPA and Ser195 as a transition-state analog, and compares the specificity pockets of thrombin and trypsin showing the S1 site of thrombin is larger. For ASH, the relevance is indirect: hirugen is a named component of the complex, though the abstract does not specify its origin or structural relationship to hirudin. The caveat is that the study is purely crystallographic/in-vitro with no therapeutic or in-vivo data.

Citation

Crystal structure of human alpha-thrombin complexed with hirugen and p-amidinophenylpyruvate at 1.6 A resolution

Chen Z et al. · Archives of biochemistry and biophysics, 1995

DOI

Added to ASH library: May 27, 2026 · Site last updated: June 18, 2026

This website provides educational information and does not constitute medical advice, diagnosis, or treatment recommendations. Medicinal leech therapy carries clinically meaningful risks and should be performed only by qualified clinicians under institutionally approved protocols. FDA 510(k) clearance for medicinal leeches is limited to specific indications; investigational and off-label discussions are labeled accordingly. For patient-specific guidance, consult a qualified healthcare provider.