2D1J

Factor Xa in complex with the inhibitor 2-[[4-[(5-chloroindol-2-yl)sulfonyl]piperazin-1-yl] carbonyl]thieno[3,2-b]pyridine n-oxide

• PDB DOI: https://doi.org/10.2210/pdb2D1J/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2005-08-24 Released: 2006-08-24 
• Deposition Author(s): Suzuki, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.232 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Design, synthesis, and biological activity of non-basic compounds as factor Xa inhibitors: SAR study of S1 and aryl binding sites.

Komoriya, S., Haginoya, N., Kobayashi, S., Nagata, T., Mochizuki, A., Suzuki, M., Yoshino, T., Horino, H., Nagahara, T., Suzuki, M., Isobe, Y., Furugoori, T.

(2005) Bioorg Med Chem 13: 3927-3954

• PubMed: 15911309 
• DOI: https://doi.org/10.1016/j.bmc.2005.04.006
• Primary Citation of Related Structures:  
  1WU1, 2D1J


• PubMed Abstract: 
  

  Compound 7 was identified as the active metabolite of 6 by HPLC and mass spectral analysis. Modification of lead compound 7 by transformation of its N-oxide 6-6 biaryl ring system and fused aromatics produced a series of non-basic fXa inhibitors with excellent potency in anti-fXa and anticoagulant assays. The optimized compounds 73b and 75b showed sub to one digit micromolar anticoagulant activity (PTCT2). Particularly, anti-fXa activity was detected in plasma of rats orally administered with 1mg/kg of compound 75b.

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Organizational Affiliation: 

Tokyo R&D Center, Daiichi Pharmaceutical Co. Ltd, 16-13 Kita-Kasai 1-Chome, Edogawa-ku, Tokyo 134-8630, Japan. [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: 32.75 kDa 
• Atom Count: 2,293 
• Modelled Residue Count: 287 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X, heavy chain	A	233	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X, light chain	B	54	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D01	E [auth A]	2-({4-[(5-CHLORO-1H-INDOL-2-YL)SULFONYL]PIPERAZIN-1-YL}CARBONYL)THIENO[3,2-B]PYRIDINE 4-OXIDE C20 H17 Cl N4 O4 S2 DHDQMXPAANQKDC-UHFFFAOYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.232 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.078	α = 90
b = 73.122	β = 90
c = 79.949	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-24 
Deposition Author(s): Suzuki, M.

Revision History  

• Version 1.0: 2006-08-24
  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: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description