Bovine Trypsin with 1-[2-[5-[amino(imino)methyl]-2-hydroxyphenoxy]-6-[3-(4,5-dihydro-1-methyl-1H-imidazol-2-yl)phenoxy]pyridin-4-yl]piperidine-3-carboxylic Acid (ZK-806974)

Experimental Data Snapshot

  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history


Crystallographic analysis of potent and selective factor Xa inhibitors complexed to bovine trypsin.

Whitlow, M.Arnaiz, D.O.Buckman, B.O.Davey, D.D.Griedel, B.Guilford, W.J.Koovakkat, S.K.Liang, A.Mohan, R.Phillips, G.B.Seto, M.Shaw, K.J.Xu, W.Zhao, Z.Light, D.R.Morrissey, M.M.

(1999) Acta Crystallogr.,Sect.D 55: 1395-1404

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Factor Xa is a serine protease which activates thrombin (factor IIa) and plays a key regulatory role in the blood-coagulation cascade. Factor Xa is, therefore, an important target for the design of anti-thrombotics. Both factor Xa and thrombin share ...

    Factor Xa is a serine protease which activates thrombin (factor IIa) and plays a key regulatory role in the blood-coagulation cascade. Factor Xa is, therefore, an important target for the design of anti-thrombotics. Both factor Xa and thrombin share sequence and structural homology with trypsin. As part of a factor Xa inhibitor-design program, a number of factor Xa inhibitors were crystallographically studied complexed to bovine trypsin. The structures of one diaryl benzimidazole, one diaryl carbazole and three diaryloxypyridines are described. All five compounds bind to trypsin in an extended conformation, with an amidinoaryl group in the S1 pocket and a second basic/hydrophobic moiety bound in the S4 pocket. These binding modes all bear a resemblance to the reported binding mode of DX-9065a in bovine trypsin and human factor Xa.

    Related Citations: 
    • Design, Synthesis, and Activity of 2,6-Diphenoxypyridine-Derived Factor Xa Inhibitors
      Phillips, G.,Davey, D.,Eagen, K.,Ng, H.P.,Pinkerton, M.,Koovakkat, S.K.,Whitlow, M.,Liang, A.,Trinh, L.,Morrissey, M.M.
      (1999) J.Med.Chem. 42: 1749
    • Discovery of N-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-3,5- Difluoro-6-[3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy] Pyridin-4-Yl-N-Methylglycine (Zk-807834): A Potent, Selective and Orally Active Inhibitor of the Blood Coagulation Enzyme Factor Xa
      Phillips, G.B.,Buckman, B.O.,Davey, D.D.,Eagen, K.A.,Guilford, W.J.,Hinchman, J.,Ho, E.,Koovakkat, S.,Liang, A.,Light, D.R.,Mohan, R.,Ng, H.P.,Post, J.,Smith, D.,Subramanyam, B.,Sullivan, M.E.,Trinh, L.,Vergona, R.,Walters, J.,White, K.,Whitlow, M.,Wu, S.,Xu, W.,Morrissey, M.M.
      (1998) J.Med.Chem. 41: 3557
    • 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 Analysis and Refinement of Two Variants of Trigonal Trypsinogen
      Bode, W.,Huber, R.
      (1978) FEBS Lett. 90: 265
    • 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
    • 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
    • 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

    Organizational Affiliation

    Berlex Biosciences, 15049 San Pablo Avenue, PO Box 4099, Richmond, California 94804, USA. marc_whitlow@berlex.com


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
223Bos taurusEC:
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on 974

Download SDF File 
Download CCD File 
C28 H27 F2 N6 O5
 Ligand Interaction
Query on CA

Download SDF File 
Download CCD File 
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
974Ki: 170 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.160α = 90.00
b = 63.780β = 90.00
c = 69.350γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

  • Deposited Date: 1999-04-28 
  • Released Date: 2000-04-29 
  • Deposition Author(s): Whitlow, M.

Revision History 

  • Version 1.0: 2000-04-29
    Type: Initial release
  • Version 1.1: 2008-01-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Database references