4AYY

Human thrombin - inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors.

Hilpert, K.Ackermann, J.Banner, D.W.Gast, A.Gubernator, K.Hadvary, P.Labler, L.Muller, K.Schmid, G.Tschopp, T.B.

(1994) J.Med.Chem. 37: 3889

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thrombin, a serine protease, plays a central role in the initiation and propagation of thrombotic events. An extensive search for new thrombin inhibitors was performed, using an unconventional approach. Screening of small basic molecules for binding ...

    Thrombin, a serine protease, plays a central role in the initiation and propagation of thrombotic events. An extensive search for new thrombin inhibitors was performed, using an unconventional approach. Screening of small basic molecules for binding in the recognition pocket of thrombin led to the discovery of (aminoiminomethyl)piperidine (amidinopiperidine) as a weak, but intrinsically selective, thrombin inhibitor. Elaboration of this molecule provided compounds which inhibit thrombin with Ki's in the range of 20-50 nM and with selectivities of 1000-4000 against trypsin. These inhibitor compounds show a new and unexpected binding mode to thrombin. Modification of the central building block and then of one of the hydrophobic substituents led to the discovery of a new family of thrombin inhibitors which has reverted to the former binding mode to thrombin. This last class of compounds shows inhibitory activities in the picomolar range, low toxicity, and a short plasma half life which favors its use for an intravenous application. From this series of thrombin inhibitors, 19f(Ro 46-6240) was selected for clinical development as an antithrombotic agent for intravenous administration.


    Organizational Affiliation

    Pharma Division, F. Hoffmann-La Roche Ltd., Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THROMBIN LIGHT CHAIN
A
30Homo 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
THROMBIN HEAVY CHAIN
B
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: 3
MoleculeChainsSequence LengthOrganismDetails
HIRUDIN-3A'
D
11Hirudo medicinalisMutation(s): 0 
Find proteins for P28508 (Hirudo medicinalis)
Go to UniProtKB:  P28508
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
9MX
Query on 9MX

Download SDF File 
Download CCD File 
B
(R)-1-[(S)-3-[((S)-1-Carbamimidoyl-piperidin-3-ylmethyl)-carbamoyl]-2-(naphthalene-2-sulfonylamino)-propionyl]-4-methyl-piperidine-2-carboxylic acid
C28 H38 N6 O6 S
BPPNPBQJRWCUDE-RJADORODSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9MXKi: 6.7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.147 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 90.800α = 90.00
b = 90.800β = 90.00
c = 132.500γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2013-08-07
    Type: Other
  • Version 1.2: 2017-06-28
    Type: Data collection