2V3O

Thrombin with 3-cycle with F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Fluorine in Pharmaceuticals: Looking Beyond Intuition.

Mueller, K.Faeh, C.Diederich, F.

(2007) Science 317: 1881

  • DOI: 10.1126/science.1131943
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fluorine substituents have become a widespread and important drug component, their introduction facilitated by the development of safe and selective fluorinating agents. Organofluorine affects nearly all physical and adsorption, distribution, metabol ...

    Fluorine substituents have become a widespread and important drug component, their introduction facilitated by the development of safe and selective fluorinating agents. Organofluorine affects nearly all physical and adsorption, distribution, metabolism, and excretion properties of a lead compound. Its inductive effects are relatively well understood, enhancing bioavailability, for example, by reducing the basicity of neighboring amines. In contrast, exploration of the specific influence of carbon-fluorine single bonds on docking interactions, whether through direct contact with the protein or through stereoelectronic effects on molecular conformation of the drug, has only recently begun. Here, we review experimental progress in this vein and add complementary analysis based on comprehensive searches in the Cambridge Structural Database and the Protein Data Bank.


    Organizational Affiliation

    Pharmaceuticals Division, Discovery Chemistry, F. Hoffmann-La Roche, CH-4070 Basel, Switzerland. klaus.mueller@roche.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THROMBIN HEAVY CHAIN
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 P01050 (Hirudo medicinalis)
Go to UniProtKB:  P01050
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
THROMBIN LIGHT CHAIN
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
NA
Query on NA

Download SDF File 
Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
I26
Query on I26

Download SDF File 
Download CCD File 
H
(2R)-[(4-CARBAMIMIDOYLPHENYL)AMINO]{3-[3-(DIMETHYLAMINO)-2,2-DIMETHYLPROPOXY]-5-ETHYL-2-FLUOROPHENYL}ETHANOIC ACID
C24 H33 F N4 O3
ZLPZGXNFKLAJEI-OAQYLSRUSA-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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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.610α = 90.00
b = 71.820β = 100.60
c = 72.280γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
CCP4phasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-24
    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: 2012-11-30
    Type: Other
  • Version 1.3: 2013-08-07
    Type: Other
  • Version 1.4: 2013-10-23
    Type: Other