1QBN

Bovine Trypsin 2-[amino(imino)methyl]-2-hydroxyphenoxy]-6-[3-(4,5-dihydro-1H-imidazol-2-yl)phenoxy]pyridine-4-carboxylic Acid (ZK-806688) Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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:  1QA0, 1QB6, 1QB9, 1QBO, 1QB1

  • 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: 
    • 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
    • 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
      Brandstetter, H.,Kuhne, A.,Bode, W.,Huber, R.,von der Saal, W.,Wirthensohn, K.,Engh, R.A.
      (1996) J.Biol.Chem. 271: 29988
    • Analytical and Production Seeding Techniques
      Stura, E.A.,Wilson, I.A.
      (1990) Methods (San Diego) 1: 38
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (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
688
Query on 688

Download SDF File 
Download CCD File 
A
2-[AMINO(IMINO)METHYL]-2-HYDROXYPHENOXY]-6-[3-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)PHENOXY]PYRIDINE-4-CARBOXYLIC ACID
ZK-806688
C22 H17 N5 O5
ILFWHJBPGCBXAY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
688Ki: 1400 nM BINDINGMOAD
688Ki: 1400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.155 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.020α = 90.00
b = 55.020β = 90.00
c = 109.140γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PROFFTrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-04-25 
  • Released Date: 2000-05-03 
  • Deposition Author(s): Whitlow, M.

Revision History 

  • Version 1.0: 2000-05-03
    Type: Initial release
  • Version 1.1: 2007-10-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance