1MTW

FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH BOVINE TRYPSIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 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

  • Primary Citation of Related Structures:  
  • Also Cited By: 1QL9, 1QL8, 1QL7, 1QBO, 1QB9

  • 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: 
    • 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 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
    • Structural Aspects of Factor Xa Inhibition
      Stubbs, M.T.
      (1996) Curr.Pharm.Des. 2: 543
    • 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
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPSIN
A
223Bos taurusEC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DX9
Query on DX9

Download SDF File 
Download CCD File 
A
(2S)-3-(7-carbamimidoylnaphthalen-2-yl)-2-[4-({(3R)-1-[(1Z)-ethanimidoyl]pyrrolidin-3-yl}oxy)phenyl]propanoic acid
DX9056A
C26 H28 N4 O3
AGRCGQSFFMCBRE-DGUCVARSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DX9Ki: 190 - 200 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.900α = 90.00
b = 61.000β = 90.00
c = 64.300γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
XDSdata reduction
XDSdata scaling
X-PLORmodel building
X-PLORrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance