1ETS

REFINED 2.3 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF BOVINE THROMBIN COMPLEXES FORMED WITH THE BENZAMIDINE AND ARGININE-BASED THROMBIN INHIBITORS NAPAP, 4-TAPAP AND MQPA: A STARTING POINT FOR IMPROVING ANTITHROMBOTICS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics.

Brandstetter, H.Turk, D.Hoeffken, H.W.Grosse, D.Sturzebecher, J.Martin, P.D.Edwards, B.F.Bode, W.

(1992) J Mol Biol 226: 1085-1099

  • DOI: 10.1016/0022-2836(92)91054-s
  • Primary Citation of Related Structures:  
    1ETT, 1ETS, 1ETR

  • PubMed Abstract: 
  • Well-diffracting crystals of bovine epsilon-thrombin in complex with several "non-peptidic" benzamidine and arginine-based thrombin inhibitors have been obtained by co-crystallization. The 2.3 A crystal structures of three complexes formed either wit ...

    Well-diffracting crystals of bovine epsilon-thrombin in complex with several "non-peptidic" benzamidine and arginine-based thrombin inhibitors have been obtained by co-crystallization. The 2.3 A crystal structures of three complexes formed either with NAPAP, 4-TAPAP, or MQPA, were solved by Patterson search methods and refined to crystallographic R-values of 0.167 to 0.178. The active-site environment of thrombin is only slightly affected by binding of the different inhibitors; in particular, the exposed "60-insertion loop" essentially maintains its typical projecting structure. The D-stereoisomer of NAPAP and the L-stereoisomer of MQPA bind to thrombin with very similar conformations, as previously inferred from their binding to bovine trypsin; the arginine side-chain of the latter inserts into the specificity pocket in a "non-canonical" manner. The L-stereoisomer of 4-TAPAP, whose binding geometry towards trypsin was only poorly defined, is bound to the thrombin active-site in a compact conformation. In contrast to NAPAP, the distal p-amidino/guanidino groups of 4-TAPAP and MQPA do not interact with the carboxylate group of Asp189 in the thrombin specificity pocket in a "symmetrical" twin N-twin O manner, but through "lateral" single N-twin O contacts; in contrast to the p-amidino group of 4-TAPAP, however, the guanidyl group of MQPA packs favourably in the pocket due to an elaborate hydrogen bond network, which includes two entrapped water molecules. These thrombin structures confirm previous conclusions of the important role of the intermolecular hydrogen bonds formed with Gly216, and of the good sterical fit of the terminal bulky hydrophobic inhibitor groups with the hydrophobic aryl binding site and the S2-cavity, respectively, for tight thrombin active site binding of these non-peptidic inhibitors. These accurate crystal structures are presumed to be excellent starting points for the design and the elaboration of improved antithrombotics.


    Related Citations: 
    • Crystallographic Determination of Thrombin Complexes with Small Synthetic Inhibitors as a Starting Point for the Receptor-Based Design of Antithrombotics
      Bode, W., Brandstetter, H., Turk, D., Bauer, M., Stuerzebecher, J.
      () To be published --: --
    • X-Ray Crystal Structure of Thrombin in Complex with D-Phe-Pro-Arg and with Small Benzamidine and Arginine-Based "Non-Peptidic" Inhibitors
      Bode, W.
      () To be published --: --
    • The Refined 1.9-Angstroms X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships
      Bode, W., Turk, D., Karshikov, A.
      (1992) Protein Sci 1: 426
    • Geometry of Binding of the Nalpha-Tosylated Piperidides of M-Amidino-, P-Amidino-and P-Guanidino Phenylalanine to Thrombin and Trypsin: X-Ray Crystal Structures of Their Trypsin Complexes and Modeling of Their Thrombin Complexes
      Turk, D., Stuerzebecher, J., Bode, W.
      (1991) FEBS Lett 287: 133
    • Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4-Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap-Thrombin and Mqpa-Thrombin
      Bode, W., Turk, D., Stuerzebecher, J.
      (1990) Eur J Biochem 193: 175
    • The Refined 1.9 Angstroms Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment
      Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S.R., Hofsteenge, J.
      (1989) EMBO J 8: 3467

    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EPSILON-THROMBINL49Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00735 (Bos taurus)
Explore P00735 
Go to UniProtKB:  P00735
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EPSILON-THROMBINH259Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00735 (Bos taurus)
Explore P00735 
Go to UniProtKB:  P00735
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MID
Query on MID

Download CCD File 
H
1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine
C27 H31 N5 O4 S
XXTWZTPVNIYSJZ-XMMPIXPASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MIDKi:  6.5   nM  BindingDB
MIDIC50:  690   nM  BindingDB
MIDIC50:  200   nM  BindingDB
MIDKi:  4   nM  BindingDB
MIDKi:  6.5   nM  BindingDB
MIDKi:  6   nM  BindingDB
MIDKi:  6000   nM  BindingDB
MIDEC50:  750   nM  BindingDB
MIDKi:  6   nM  Binding MOAD
MIDKi:  6   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.73α = 90
b = 88.73β = 90
c = 102.9γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other