3F68

Thrombin Inhibition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin.

Baum, B.Muley, L.Heine, A.Smolinski, M.Hangauer, D.Klebe, G.

(2009) J.Mol.Biol. 391: 552-564

  • DOI: 10.1016/j.jmb.2009.06.016
  • Primary Citation of Related Structures:  2ZC9, 2ZDA, 2ZFP, 2ZGX, 2ZO3, 3DHK, 3DUX

  • PubMed Abstract: 
  • Successful design of potent and selective protein inhibitors, in terms of structure-based drug design, strongly relies on the correct understanding of the molecular features determining the ligand binding to the target protein. We present a case stud ...

    Successful design of potent and selective protein inhibitors, in terms of structure-based drug design, strongly relies on the correct understanding of the molecular features determining the ligand binding to the target protein. We present a case study of serine protease inhibitors with a bis(phenyl)methane moiety binding into the S3 pocket. These inhibitors bind with remarkable potency to the active site of thrombin, the blood coagulation factor IIa. A combination of X-ray crystallography and isothermal titration calorimetry provides conclusive insights into the driving forces responsible for the surprisingly high potency of these inhibitors. Analysis of six well-resolved crystal structures (resolution 1.58-2.25 A) along with the thermodynamic data allows an explanation of the tight binding of the bis(phenyl)methane inhibitors. Interestingly, the two phenyl rings contribute to binding affinity for very different reasons - a fact that can only be elucidated by a structure-based approach. The first phenyl moiety occupies the hydrophobic S3 pocket, resulting in a mainly entropic advantage of binding. This observation is based on the displacement of structural water molecules from the S3 pocket that are observed in complexes with inhibitors that do not bind in the S3 pocket. The same classic hydrophobic effect cannot explain the enhanced binding affinity resulting from the attachment of the second, more solvent-exposed phenyl ring. For the bis(phenyl)methane inhibitors, an observed adaptive rotation of a glutamate residue adjacent to the S3 binding pocket attracted our attention. The rotation of this glutamate into salt-bridging distance with a lysine moiety correlates with an enhanced enthalpic contribution to binding for these highly potent thrombin binders. This explanation for the magnitude of the attractive force is confirmed by data retrieved by a Relibase search of several thrombin-inhibitor complexes deposited in the Protein Data Bank exhibiting similar molecular features. Special attention was attributed to putative changes in the protonation states of the interaction partners. For this purpose, two analogous inhibitors differing mainly in their potential to change the protonation state of a hydrogen-bond donor functionality were compared. Buffer dependencies of the binding enthalpy associated with complex formation could be traced by isothermal titration calorimetry, which revealed, along with analysis of the crystal structures (resolution 1.60 and 1.75 A), that a virtually compensating proton interchange between enzyme, inhibitor and buffer is responsible for the observed buffer-independent thermodynamic signatures.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, Philipps-University Marburg, 35032 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
L
36Homo sapiensGene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
H
259Homo sapiensGene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hirudin variant-2
I
11Hirudo medicinalisN/A
Find proteins for P09945 (Hirudo medicinalis)
Go to UniProtKB:  P09945
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
91U
Query on 91U

Download SDF File 
Download CCD File 
H
N-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide
C23 H32 Cl N3 O3
NEBILTDHZWSWJN-RTWAWAEBSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000611 (91U)
Query on PRD_000611
HN-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamidePeptide-like / Thrombin inhibitor

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
I
L-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
91UKi: 8700 nM BINDINGMOAD
91UKi: 8700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.280α = 90.00
b = 71.950β = 100.05
c = 72.500γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
MOSFLMdata reduction
CNSphasing
SCALEPACKdata scaling
MAR345data collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Type: Other
  • Version 1.3: 2016-10-26
    Type: Structure summary
  • Version 1.4: 2017-10-25
    Type: Refinement description