3LC5 | pdb_00003lc5

Selective Benzothiophine Inhibitors of Factor IXa

• PDB DOI: https://doi.org/10.2210/pdb3LC5/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-09 Released: 2010-02-23 
• Deposition Author(s): Wang, S., Beck, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.277 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Structure Based Drug Design: Development of Potent and Selective Factor IXa (FIXa) Inhibitors.

Wang, S., Beck, R., Burd, A., Blench, T., Marlin, F., Ayele, T., Buxton, S., Dagostin, C., Malic, M., Joshi, R., Barry, J., Sajad, M., Cheung, C., Shaikh, S., Chahwala, S., Chander, C., Baumgartner, C., Holthoff, H.P., Murray, E., Blackney, M., Giddings, A.

(2010) J Med Chem 53: 1473-1482

• PubMed: 20121197 
• DOI: https://doi.org/10.1021/jm901476x
• Primary Citation Related Structures: 
  3LC5


• PubMed Abstract: 
  

  On the basis of our understanding on the binding interactions of the benzothiophene template within the FIXa active site by X-ray crystallography and molecular modeling studies, we developed our SAR strategy by targeting the 4-position of the template to access the S1 beta and S2-S4 sites. A number of highly selective and potent factor Xa (FXa) and FIXa inhibitors were identified by simple switch of functional groups with conformational changes toward the S2-S4 sites.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Trigen Ltd., Emmanuel Kaye Building, 1B Manresa Road,London SW3 6LR, UK. [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: 32.92 kDa 
• Atom Count: 2,296 
• Modeled Residue Count: 289 
• Deposited Residue Count: 292 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	A	235	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	B	57	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IZX	D [auth A]	1-{4-[(R)-phenyl(3-phenyl-1,2,4-oxadiazol-5-yl)methoxy]-1-benzothiophen-2-yl}methanediamine C24 H20 N4 O2 S VBSNODZWDZSFEZ-OAQYLSRUSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.277 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.12	α = 90
b = 65.738	β = 90
c = 93.985	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Wang, S., Beck, R.

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary