PDBsum entry 1tnj

Hydrolase/hydrolase inhibitor

PDB id: 1tnj

Contents

Protein chain

223 a.a.

Ligands

PEA

Metals

_CA

Waters ×489

References listed in PDB file

Key reference

• Title: Prediction of new serine proteinase inhibitors.
• Authors: I.V.Kurinov, R.W.Harrison.
• Ref.: Nat Struct Biol, 1994, 1, 735-743.
• PubMed id: 7634078

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 89%.

Abstract

We describe here the use of a rapid computational method to predict the relative binding strengths of a series of small-molecule ligands for the serine proteinase trypsin. Flexible molecular models of the ligands were docked to the proteinase using an all-atom potential set, without cutoff limits for the non-bonded and electrostatic energies. The binding-strength calculation is done directly in terms of a molecular mechanics potential. The binding of eighteen different compounds, including non-binding controls, has been successfully predicted. The measured Ki is correlated with the predicted energy. The correctness of the theoretical calculations is demonstrated with both kinetics measurements and X-ray structure determination of six enzyme-inhibitor complexes.