Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23835.84 
• Atom Count: 1671 
• Residue Count: 223 
• Unique protein chains: 1

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

• DOI: 10.2210/pdb1QBN/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus


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

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Experimental Data Snapshot

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

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

• PubMed: 10417407 
• DOI: 10.1107/s0907444999007350
• Primary Citation of Related Structures:  
  1QA0, 1QB1, 1QBO, 1QB9, 1QB6


• 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 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.

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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
• 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
• 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
• 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
• Analytical and Production Seeding Techniques
  Stura, E.A.,Wilson, I.A.
  (1990) Methods (San Diego) 1: 38




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Organizational Affiliation: 

Berlex Biosciences, 15049 San Pablo Avenue, PO Box 4099, Richmond, California 94804, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (TRYPSIN)	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
Find proteins for P00760 (Bos taurus) Go to UniProtKB:  P00760

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
688	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
688	Ki: 1400 nM BINDINGMOAD
688	Ki: 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 = 55.020	α = 90.00
b = 55.020	β = 90.00
c = 109.140	γ = 120.00

Software Package:

Software Name	Purpose
DENZO	data reduction
PROFFT	refinement
SCALEPACK	data scaling

Structure Validation

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