Biological Assembly 1  

 3D View: Structure | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.84 kDa 
• Atom Count: 1836 
• Modelled Residue Count: 223 
• Deposited 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
• Mutation(s): No 


• 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: 1.80 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 D Biol Crystallogr 55: 1395-1404

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


• 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: 

• Crystal Structure Analysis and Refinement of Two Variants of Trigonal Trypsinogen
  Bode, W., Huber, R.
  (1978) FEBS Lett 90: 265

• 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

• 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

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

• 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

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Organizational Affiliation: 

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
688 (Subject of Investigation/LOI)	D [auth A]	2-[AMINO(IMINO)METHYL]-2-HYDROXYPHENOXY]-6-[3-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)PHENOXY]PYRIDINE-4-CARBOXYLIC ACID C22 H17 N5 O5 ILFWHJBPGCBXAY-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
688	Binding MOAD:  1QBN	Ki: 1400 (nM) from 1 assay(s)
	PDBBind:  1QBN	Ki: 1400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.217 
• R-Value Work: 0.155 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.02	α = 90
b = 55.02	β = 90
c = 109.14	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PROFFT	refinement

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