2CN0

Complex of Recombinant Human Thrombin with a Designed Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Mapping the Fluorophilicity of a Hydrophobic Pocket: Synthesis and Biological Evaluation of Tricyclic Thrombin Inhibitors Directing Fluorinated Alkyl Groups Into the P Pocket

Hoffmann-Roder, A.Schweizer, E.Egger, J.Seiler, P.Obst-Sander, U.Wagner, B.Kansy, M.Banner, D.W.Diederich, F.

(2006) Chemmedchem 1: 1205

  • DOI: 10.1002/cmdc.200600124

  • PubMed Abstract: 
  • In the completion of our fluorine scan of tricyclic inhibitors to map the fluorophilicity/fluorophobicity of the thrombin active site, a series of 11 new ligands featuring alkyl, alkenyl, and fluoroalkyl groups was prepared to explore fluorine effect ...

    In the completion of our fluorine scan of tricyclic inhibitors to map the fluorophilicity/fluorophobicity of the thrombin active site, a series of 11 new ligands featuring alkyl, alkenyl, and fluoroalkyl groups was prepared to explore fluorine effects on binding into the hydrophobic proximal (P) pocket, lined by Tyr 60A and Trp 60D, His 57, and Leu 99. The synthesis of the tricyclic scaffolds was based on the 1,3-dipolar cycloaddition of azomethine ylides, derived from L-proline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide. Introduction of alkyl, alkenyl, and partially fluorinated alkyl residues was achieved upon substitution of a sulfonyl group by mixed Mg/Zn organometallics followed by oxidation/deoxyfluorination, as well as oxidation/reduction/deoxyfluorination sequences. In contrast, the incorporation of perfluoroalkyl groups required a stereoselective nucleophilic addition reaction at the "upper" carbonyl group of the tricycles, thereby yielding scaffolds with an additional OH, F, or OMe group, respectively. All newly prepared inhibitors showed potent biological activity, with inhibitory constants (K(i) values) in the range of 0.008-0.163 microM. The X-ray crystal structure of a protein-ligand complex revealed the exact positioning of a difluoromethyl substituent in the tight P pocket. Fluorophilic characteristics are attributed to this hydrophobic pocket, although the potency of the inhibitors was found to be modulated by steric rather than electronic factors.


    Organizational Affiliation

    Institut für Organische Chemie, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTHROMBIN PRECURSOR
H
257Homo sapiensMutation(s): 0 
Gene 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
HIRUDIN IIA
I
11Hirudo medicinalisMutation(s): 0 
Find proteins for P09945 (Hirudo medicinalis)
Go to UniProtKB:  P09945
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTHROMBIN PRECURSOR
L
28Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F25
Query on F25

Download SDF File 
Download CCD File 
H
4-(1R,3AS,4R,8AS,8BR)-[1-DIFLUOROMETHYL-2-(4-FLUOROBENZYL)-3-OXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4-YL]BENZAMIDINE
C24 H27 F3 N4 O
VPNYXOTTXAXSIH-SXYSDOLCSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000481
Query on PRD_000481
IN-terminal Asp des-amino Hirudin-3A'Oligopeptide / Anticoagulant, Antithrombotic

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F25Ki: 22 nM BINDINGMOAD
F25Ki: 22 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.640α = 90.00
b = 71.410β = 100.35
c = 72.520γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Type: Other
  • Version 1.3: 2013-08-07
    Type: Derived calculations, Other
  • Version 1.4: 2013-10-23
    Type: Other
  • Version 1.5: 2017-03-29
    Type: Source and taxonomy, Structure summary