1TX8

Bovine Trypsin complexed with AMSO

• PDB DOI: https://doi.org/10.2210/pdb1TX8/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2004-07-02 Released: 2005-10-18 
• Deposition Author(s): Mesecar, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis, and evaluation of oxyanion-hole selective inhibitor substituents for the S1 subsite of factor Xa

Rumthao, S., Lee, O., Sheng, Q., Fu, W., Mulhearn, D.C., Crich, D., Mesecar, A.D., Johnson, M.E.

(2004) Bioorg Med Chem Lett 14: 5165-5170

• PubMed: 15380220 
• DOI: https://doi.org/10.1016/j.bmcl.2004.07.054
• Primary Citation of Related Structures:  
  1TX8


• PubMed Abstract: 
  

  We have designed, synthesized, and evaluated the factor Xa inhibitory activities of p-amidinophenyl-sulfones, amines, and alcohols intended to take advantage of the polarity and hydrogen-bonding potential of the oxyanion hole region of the S1 specificity pocket. We demonstrate that placement of an anionic group within the oxyanion hole region of the catalytic site substantially enhances activity, with small flexible groups favored over bulkier ones. Ab initio pKa calculations suggest that the hydroxyl substituent frequently used for benzamidine moieties may be ionized to form an anionic group, consistent with the general trend. One nonamidine based substituent also shows promising activity.

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Organizational Affiliation: 

Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 S. Ashland Avenue, m/c 870, Chicago, IL 60607-7173, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.56 kDa 
• Atom Count: 1,812 
• Modelled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsinogen	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
AM4	C [auth A]	4-(METHYLSULFONYL)BENZENECARBOXIMIDAMIDE C8 H10 N2 O2 S ANPBNAUKOUYEGJ-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.795	α = 90
b = 58.58	β = 90
c = 67.563	γ = 90

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-18 
Deposition Author(s): Mesecar, A.D.

Revision History  

• Version 1.0: 2005-10-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary