1QA0 | pdb_00001qa0

BOVINE TRYPSIN 2-AMINOBENZIMIDAZOLE COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1QA0/pdb

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


• Deposited: 1999-04-09 Released: 2000-04-10 
• Deposition Author(s): Whitlow, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 
  0.172 (Depositor) 
• R-Value Observed: 
  0.172 (Depositor) 

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: https://doi.org/10.1107/s0907444999007350
• Primary Citation 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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Organizational Affiliation: 
• Berlex Biosciences, 15049 San Pablo Avenue, PO Box 4099, Richmond, California 94804, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.5 kDa 
• Atom Count: 1,765 
• Modeled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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
AX7	C [auth A]	1H-benzimidazol-2-amine C7 H7 N3 JWYUFVNJZUSCSM-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work:  0.172 (Depositor) 
• R-Value Observed: 0.172 (Depositor) 

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
PROFFT	refinement
XTALVIEW	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-04-10 
Deposition Author(s): Whitlow, M.

Revision History  

• Version 1.0: 2000-04-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.5: 2024-03-13
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 1.6: 2024-11-06
  Changes: Structure summary
• Version 2.0: 2025-08-13
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary