1JWT

CRYSTAL STRUCTURE OF THROMBIN IN COMPLEX WITH A NOVEL BICYCLIC LACTAM INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Novel bicyclic lactam inhibitors of thrombin: potency and selectivity optimization through P1 residues.

Levesque, S.St-Denis, Y.Bachand, B.Preville, P.Leblond, L.Winocour, P.D.Edmunds, J.J.Rubin, J.R.Siddiqui, M.A.

(2001) Bioorg.Med.Chem.Lett. 11: 3161-3164


  • PubMed Abstract: 
  • Peptidomimetic inhibitors of thrombin lacking the important Ser195-carbonyl interaction have been prepared. The binding energy lost after the removal of the activated carbonyl was recaptured through a series of modifications of the P1 residues of the ...

    Peptidomimetic inhibitors of thrombin lacking the important Ser195-carbonyl interaction have been prepared. The binding energy lost after the removal of the activated carbonyl was recaptured through a series of modifications of the P1 residues of the bicyclic lactam inhibitors. Selected substituted compounds displayed useful pharmacological profiles both in vitro and in vivo.


    Organizational Affiliation

    Shire BioChem Inc., 275 Armand-Frappier Blvd., Laval, H7V 4A7, Qu├ębec, Canada. slevesque@ca.shire.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
A
305Homo sapiensGene 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLI
Query on BLI

Download SDF File 
Download CCD File 
A
4-OXO-2-PHENYLMETHANESULFONYL-OCTAHYDRO-PYRROLO[1,2-A]PYRAZINE-6-CARBOXYLIC ACID [1-(N-HYDROXYCARBAMIMIDOYL)-PIPERIDIN-4-YLMETHYL]-AMIDE
C22 H32 N6 O5 S
DHTSUHWLPAEEQB-OALUTQOASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BLIKi: 14 nM BINDINGMOAD
BLIKi: 14 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.540α = 90.00
b = 72.180β = 100.99
c = 73.410γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
AUTOMARdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description