2ZQ1

Exploring trypsin S3 pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties

Brandt, T.Holzmann, N.Muley, L.Khayat, M.Wegscheid-Gerlach, C.Baum, B.Heine, A.Hangauer, D.Klebe, G.

(2011) J.Mol.Biol. 405: 1170-1187

  • DOI: 10.1016/j.jmb.2010.11.038
  • Primary Citation of Related Structures:  2ZDK, 2ZDL, 2ZDM, 2ZDN, 2ZFS, 2ZFT, 2ZHD, 2ZQ2, 3LJJ, 3LJO

  • PubMed Abstract: 
  • A congeneric series of benzamidine-type ligands with a central proline moiety and a terminal cycloalkyl group--linked by a secondary amine, ether, or methylene bridge--was synthesized as trypsin inhibitors. This series of inhibitors was investigated ...

    A congeneric series of benzamidine-type ligands with a central proline moiety and a terminal cycloalkyl group--linked by a secondary amine, ether, or methylene bridge--was synthesized as trypsin inhibitors. This series of inhibitors was investigated by isothermal titration calorimetry, crystal structure analysis in two crystal forms, and molecular dynamics simulations. Even though all of these congeneric ligands exhibited essentially the same affinity for trypsin, their binding profiles at the structural, dynamic, and thermodynamic levels are very distinct. The ligands display a pronounced enthalpy/entropy compensation that results in a nearly unchanged free energy of binding, even though individual enthalpy and entropy terms change significantly across the series. Crystal structures revealed that the secondary amine-linked analogs scatter over two distinct conformational families of binding modes that occupy either the inside or of the outside the protein's S3/S4 specificity pocket. In contrast, the ether-linked and methylene-linked ligands preferentially occupy the hydrophobic specificity pocket. This also explains why the latter ligands could only be crystallized in the conformationally restricting closed crystal form whereas the derivative with the highest residual mobility in the series escaped our attempts to crystallize it in the closed form; instead, a well-resolved structure could only be achieved in the open form with the ligand in disordered orientation. These distinct binding modes are supported by molecular dynamics simulations and correlate with the shifting enthalpic/entropic signatures of ligand binding. The examples demonstrate that, at the molecular level, binding modes and thermodynamic binding signatures can be very different even for closely related ligands. However, deviating binding profiles provide the opportunity to optimally address a given target.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cationic trypsin
A
223Bos taurusEC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
11U
Query on 11U

Download SDF File 
Download CCD File 
A
(S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclohexylamino)ethanoyl)pyrrolidine-2-carboxamide
(2S)-1-[cyclohexylamino)acetyl-N-{4-[amino(imino)methyl]benzyl}pyrrolidine-2-carboxamide
C21 H31 N5 O2
RYKFVFFOIYLADT-SFHVURJKSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000587 (11U)
Query on PRD_000587
A(S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclohexylamino)ethanoyl)pyrrolidine-2-carboxamidePeptide-like / Thrombin inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
11UKd: 239 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.149 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 54.900α = 90.00
b = 54.900β = 90.00
c = 109.000γ = 120.00
Software Package:
Software NamePurpose
SHELXmodel building
MAR345data collection
CNSphasing
HKL-2000data scaling
HKL-2000data reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2013-02-27
    Type: Other
  • Version 1.3: 2014-01-22
    Type: Database references
  • Version 1.4: 2017-10-11
    Type: Refinement description