1QJ6

Novel Covalent Active Site Thrombin Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Crystal Structures of Thrombin Complexed to a Novel Series of Synthetic Inhibitors Containing a 5,5-Trans-Lactone Template

Jhoti, H.Cleasby, A.Reid, S.Thomas, P.Weir, M.Wonacott, A.

(1999) Biochemistry 38: 7969

  • DOI: 10.1021/bi9830359
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The binding modes of four active site-directed, acylating inhibitors of human alpha-thrombin have been determined using X-ray crystallography. These inhibitors (GR157368, GR166081, GR167088, and GR179849) are representatives of a series utilizing a n ...

    The binding modes of four active site-directed, acylating inhibitors of human alpha-thrombin have been determined using X-ray crystallography. These inhibitors (GR157368, GR166081, GR167088, and GR179849) are representatives of a series utilizing a novel 5, 5-trans-lactone template to specifically acylate Ser195 of thrombin, resulting in an acyl complex. In each case the crystal structure of the complex reveals a binding mode which is consistent with the formation of a covalent bond between the ring-opened lactone of the inhibitor and residue Ser195. Improvements in potency and selectivity of these inhibitors for thrombin are rationalized on the basis of the observed protein/inhibitor interactions identified in these complexes. Occupation of the thrombin S2 and S3 pockets is shown to be directly correlated with improved binding and a degree of selectivity. The binding mode of GR179849 to thrombin is compared with the thrombin/PPACK complex [Bode, W., Turk, D., and Karshikov, A. (1992) Protein Sci. 1, 426-471] as this represents the archetypal binding mode for a thrombin inhibitor. This series of crystal structures is the first to be reported of synthetic, nonpeptidic acylating inhibitors bound to thrombin and provides details of the molecular recognition features that resulted in nanomolar potency.


    Organizational Affiliation

    Biomolecular Structure Unit, Glaxo Wellcome Medicines Research Centre, Hertfordshire, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THROMBIN
A
36Homo 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
B
259Homo 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
HIRUGEN
I
10Hirudo medicinalisMutation(s): 0 
Find proteins for P01050 (Hirudo medicinalis)
Go to UniProtKB:  P01050
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
167
Query on 167

Download SDF File 
Download CCD File 
B
6-CARBAMIMIDOYL-2-[2-HYDROXY-5-(3-METHOXY-PHENYL)-INDAN-1-YL]-HEXANOIC ACID
GR167088
C23 H28 N2 O4
NMOUMGFCBOWPAB-RZUBCFFCSA-N
 Ligand Interaction
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 %)
167IC50: 18 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.800α = 90.00
b = 72.000β = 101.00
c = 73.200γ = 90.00
Software Package:
Software NamePurpose
MADNESSdata reduction
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-06-22 
  • Released Date: 2000-06-22 
  • Deposition Author(s): Jhoti, H., Cleasby, A.

Revision History 

  • Version 1.0: 2000-06-22
    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: 2013-03-13
    Type: Other
  • Version 1.4: 2017-07-12
    Type: Refinement description
  • Version 1.5: 2018-05-30
    Type: Data collection, Structure summary