5TNO

Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors

• PDB DOI: https://doi.org/10.2210/pdb5TNO/pdb

• Classification: HYDROLASE/HYDROLASE inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-10-14 Released: 2017-04-26 
• Deposition Author(s): Sakurada, I., Endo, T., Hikita, K., Hirabayashi, T., Hosaka, Y., Kato, Y., Maeda, Y., Matsumoto, S., Mizuno, T., Nagasue, H., Nishimura, T., Shimada, S., Shinozaki, M., Taguchi, K., Takeuchi, K., Yokoyama, T., Hruza, A., Reichert, P., Zhang, T., Wood, H.B., Nakao, K., Furusako, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.158 
• R-Value Work: 0.145 
• R-Value Observed: 0.145 

Starting Model: experimental

Literature

Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors.

Sakurada, I., Endo, T., Hikita, K., Hirabayashi, T., Hosaka, Y., Kato, Y., Maeda, Y., Matsumoto, S., Mizuno, T., Nagasue, H., Nishimura, T., Shimada, S., Shinozaki, M., Taguchi, K., Takeuchi, K., Yokoyama, T., Hruza, A., Reichert, P., Zhang, T., Wood, H.B., Nakao, K., Furusako, S.

(2017) Bioorg Med Chem Lett 27: 2622-2628

• PubMed: 28408226 
• DOI: https://doi.org/10.1016/j.bmcl.2017.03.002
• Primary Citation of Related Structures:  
  5TNO, 5TNT


• PubMed Abstract: 
  

  Using structure based drug design, novel aminobenzisoxazoles as coagulation factor IXa inhibitors were designed and synthesized. Highly selective inhibition of FIXa over FXa was demonstrated. Anticoagulation profile of selected compounds was evaluated by aPTT and PT tests. In vitro ADMET and pharmacokinetic (PK) profiles were also evaluated.

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Organizational Affiliation: 

Discovery Research, Mochida Pharmaceutical Co. Ltd., 722 Uenohara, Jimba, Gotemba, Shizuoka 412-8524, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.38 kDa 
• Atom Count: 2,568 
• Modelled Residue Count: 286 
• Deposited Residue Count: 297 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	A	235	Homo sapiens	Mutation(s): 1  Gene Names: F9 EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens) Explore P00740  Go to UniProtKB:  P00740
PHAROS:  P00740 GTEx:  ENSG00000101981

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	B	62	Homo sapiens	Mutation(s): 0  Gene Names: F9 EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens) Explore P00740  Go to UniProtKB:  P00740
PHAROS:  P00740 GTEx:  ENSG00000101981

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	E [auth A], F [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
UNL	C [auth A]	Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.158 
• R-Value Work: 0.145 
• R-Value Observed: 0.145 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.835	α = 90
b = 98.835	β = 90
c = 94.252	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data scaling
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Sakurada, I., Endo, T., Hikita, K., Hirabayashi, T., Hosaka, Y., Kato, Y., Maeda, Y., Matsumoto, S., Mizuno, T., Nagasue, H., Nishimura, T., Shimada, S., Shinozaki, M., Taguchi, K., Takeuchi, K., Yokoyama, T., Hruza, A., Reichert, P., Zhang, T., Wood, H.B., Nakao, K., Furusako, S.

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2017-05-24
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary