1BHX

X-RAY STRUCTURE OF THE COMPLEX OF HUMAN ALPHA THROMBIN WITH THE INHIBITOR SDZ 229-357


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Rational design, synthesis, and X-ray structure of selective noncovalent thrombin inhibitors.

Wagner, J.Kallen, J.Ehrhardt, C.Evenou, J.P.Wagner, D.

(1998) J.Med.Chem. 41: 3664-3674

  • DOI: 10.1021/jm981013e

  • PubMed Abstract: 
  • We have designed, synthesized, and tested in vitro a novel class of noncovalent thrombin inhibitors. The main feature of these inhibitors is a 6,5-fused bicyclic core structure that fills the S2 pocket of the active site of thrombin. The bicycle intr ...

    We have designed, synthesized, and tested in vitro a novel class of noncovalent thrombin inhibitors. The main feature of these inhibitors is a 6,5-fused bicyclic core structure that fills the S2 pocket of the active site of thrombin. The bicycle introduces conformational constraint into the ligand and locks the Xaa-Pro amide bond into the desired trans configuration. Among the known ring systems, we selected by molecular modeling the 7-thiaindolizidinones (BTD) as our basic template. The influence of several structural features was analyzed: the length of the argininal side chain, the stereochemistry at C6, and the importance of making optimal use of the S3 pocket. Finally, an X-ray crystal structure of inhibitor 15 bound to thrombin was obtained at a resolution of 2.3 A. These designed thrombin inhibitors, which were prepared by an efficient synthesis, showed high selectivity over trypsin and other serine proteases. Further derivation based on the information obtained by X-ray crystallography should certainly allow to improve the potency.


    Organizational Affiliation

    Novartis Pharma AG, CH-4002 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA THROMBIN
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
ALPHA THROMBIN
B
147Homo 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
ALPHA THROMBIN
F
105Homo 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: 4
MoleculeChainsSequence LengthOrganismDetails
ALPHA THROMBIN
E
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R56
Query on R56

Download SDF File 
Download CCD File 
F
5-OXO-6-PHENYLMETHANESULFONYLAMINO-HEXAHYDRO-THIAZOLO[3,2-A]PYRIDINE-3-CARBOXYLIC ACID (3-GUANIDINO-PROPYL)-AMIDE
C19 H28 N6 O4 S2
SOIIHESTBYNJRH-PMPSAXMXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
R56Ki: 145 nM BINDINGMOAD
R56Ki: 145 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.000α = 90.00
b = 72.200β = 100.70
c = 73.100γ = 90.00
Software Package:
Software NamePurpose
MADNESdata reduction
PROCORdata scaling
Agrovatadata reduction
X-PLORmodel building
MADNESdata collection
PROCORdata reduction
X-PLORphasing
Agrovatadata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-06-10 
  • Released Date: 1998-11-04 
  • Deposition Author(s): Kallen, J.

Revision History 

  • Version 1.0: 1998-11-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2018-04-18
    Type: Data collection, Other, Refinement description