1MTW

FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH BOVINE TRYPSIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of factor Xa specific inhibitors in complex with trypsin: structural grounds for inhibition of factor Xa and selectivity against thrombin.

Stubbs, M.T.Huber, R.Bode, W.

(1995) FEBS Lett 375: 103-107

  • DOI: 10.1016/0014-5793(95)01190-p
  • Primary Citation of Related Structures:  
    1MTW, 1MTV, 1MTU, 1MTS

  • PubMed Abstract: 
  • Crystal structures of DX9065a and a related bisamidino-aryl inhibitor specific for the blood-clotting factor Xa have been solved in complex with bovine beta-trypsin to a resolution of 1.9 A. Each inhibitor exhibits an extended conformation along the ...

    Crystal structures of DX9065a and a related bisamidino-aryl inhibitor specific for the blood-clotting factor Xa have been solved in complex with bovine beta-trypsin to a resolution of 1.9 A. Each inhibitor exhibits an extended conformation along the active site, in contrast to the compact folded structures observed for thrombin specific inhibitors. Few direct contacts (predominantly in the S1 pocket) are made between trypsin and the inhibitors. Transfer of the inhibitors to the active site of factor Xa suggests a three-site interaction: salt bridge formation at the base of the primary specificity pocket, extensive hydrophobic surface burial and a weak electrostatic interaction between the distal basic component of the inhibitor and an electronegative cavity of factor Xa formed by three backbone carbonyl oxygens. Additivity of these three interactions is the basis for the observed strong inhibition of factor Xa and provides a framework for the design of novel factor Xa inhibitors. A propionic acid group of the inhibitor would clash with the thrombin specific '60-insertion loop', thus conferring selectivity against thrombin.


    Related Citations: 
    • The Second Kunitz Domain of Human Tissue Factor Pathway Inhibitor. Cloning, Structure Determination and Interaction with Factor Xa
      Burgering, M.J., Orbons, L.P., Van Der Doelen, A., Mulders, J., Theunissen, H.J., Grootenhuis, P.D., Bode, W., Huber, R., Stubbs, M.T.
      (1997) J Mol Biol 269: 395
    • The Ornithodorin-Thrombin Crystal Structure, a Key to the Tap Enigma?
      Van De Locht, A., Stubbs, M.T., Bode, W., Friedrich, T., Bollschweiler, C., Hoffken, W., Huber, R.
      (1996) EMBO J 15: 6011
    • Structural Aspects of Factor Xa Inhibition
      Stubbs, M.T.
      (1996) Curr Pharm Des 2: 543
    • X-Ray Structure of Active Site-Inhibited Clotting Factor Xa. Implications for Drug Design and Substrate Recognition
      Brandstetter, H., Kuhne, A., Bode, W., Huber, R., Von Der Saal, W., Wirthensohn, K., Engh, R.A.
      (1996) J Biol Chem 271: 29988
    • Structure of Human Des(1-45) Factor Xa at 2.2 A Resolution
      Padmanabhan, K., Padmanabhan, K.P., Tulinsky, A., Park, C.H., Bode, W., Huber, R., Blankenship, D.T., Cardin, A.D., Kisiel, W.
      (1993) J Mol Biol 232: 947
    • Geometry of Binding of the N Alpha-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., Sturzebecher, 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 to Carboxylic Acid (Mqpa) Human Alpha-Thrombin. X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap-Thrombin and Mqpa-Thrombin
      Bode, W., Turk, D., Sturzebecher, J.
      (1990) Eur J Biochem 193: 175
    • Crystal Structure of Bovine Beta-Trypsin at 1.5 A Resolution in a Crystal Form with Low Molecular Packing Density. Active Site Geometry, Ion Pairs and Solvent Structure
      Bartunik, H.D., Summers, L.J., Bartsch, H.H.
      (1989) J Mol Biol 210: 813
    • The Refined Crystal Structure of Bovine Beta-Trypsin at 1.8 A Resolution. II. Crystallographic Refinement, Calcium Binding Site, Benzamidine Binding Site and Active Site at Ph 7.0
      Bode, W., Schwager, P.
      (1975) J Mol Biol 98: 693

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRYPSINA223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DX9
Query on DX9

Download CCD File 
A
(2S)-3-(7-carbamimidoylnaphthalen-2-yl)-2-[4-({(3R)-1-[(1Z)-ethanimidoyl]pyrrolidin-3-yl}oxy)phenyl]propanoic acid
C26 H28 N4 O3
AGRCGQSFFMCBRE-DGUCVARSSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DX9Ki:  200   nM  BindingDB
DX9Ki:  190   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.9α = 90
b = 61β = 90
c = 64.3γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XSCALEdata scaling
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1997-05-16 
  • Released Date: 1997-11-12 
  • Deposition Author(s): Stubbs, M.T.

Revision History 

  • Version 1.0: 1997-11-12
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance