PDBsum entry 3pyh

Hydrolase/hydrolase inhibitor

PDB id: 3pyh

Contents

Protein chain

223 a.a.

Ligands

3YH

SO4

Metals

_CL

_CA

Waters ×264

PDB id:

3pyh

Name:

Hydrolase/hydrolase inhibitor

Title:

Bovine trypsin variant x(tripleglu217ile227) in complex with small molecule inhibitor

Structure:

Cationic trypsin. Chain: a. Fragment: unp residues 24-246. Synonym: beta-trypsin, alpha-trypsin chain 1, alpha-trypsin chain 2. Engineered: yes. Mutation: yes

Source:

Bos taurus. Bovine. Organism_taxid: 9913. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.159 R-free: 0.218

Authors:

A.Tziridis,P.Neumann,P.Kolenko,M.T.Stubbs

Key ref:

A.Tziridis et al. (2014). Correlating structure and ligand affinity in drug discovery: a cautionary tale involving second shell residues. Biol Chem, 395, 891-903. PubMed id: 25003390 DOI: 10.1515/hsz-2014-0158

Date:

13-Dec-10 Release date: 21-Dec-11

Protein chain

P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus

Seq: 246 a.a.

Struc: 223 a.a.*

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.21.4 - trypsin.
• Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

DOI no: 10.1515/hsz-2014-0158

Biol Chem 395:891-903 (2014)

PubMed id: 25003390

Correlating structure and ligand affinity in drug discovery: a cautionary tale involving second shell residues.

A.Tziridis, D.Rauh, P.Neumann, P.Kolenko, A.Menzel, U.Bräuer, C.Ursel, P.Steinmetzer, J.Stürzebecher, A.Schweinitz, T.Steinmetzer, M.T.Stubbs.

ABSTRACT

Abstract A high-resolution crystallographic structure determination of a protein-ligand complex is generally accepted as the 'gold standard' for structure-based drug design, yet the relationship between structure and affinity is neither obvious nor straightforward. Here we analyze the interactions of a series of serine proteinase inhibitors with trypsin variants onto which the ligand-binding site of factor Xa has been grafted. Despite conservative mutations of only two residues not immediately in contact with ligands (second shell residues), significant differences in the affinity profiles of the variants are observed. Structural analyses demonstrate that these are due to multiple effects, including differences in the structure of the binding site, differences in target flexibility and differences in inhibitor binding modes. The data presented here highlight the myriad competing microscopic processes that contribute to protein-ligand interactions and emphasize the difficulties in predicting affinity from structure.