3Q3K | pdb_00003q3k

Factor Xa in complex with a phenylenediamine derivative

• PDB DOI: https://doi.org/10.2210/pdb3Q3K/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2010-12-22 Released: 2011-12-28 
• Deposition Author(s): Suzuki, M., Imai, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.216 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis and SAR of novel ethylenediamine and phenylenediamine derivatives as factor Xa inhibitors.

Yoshikawa, K., Yoshino, T., Yokomizo, Y., Uoto, K., Naito, H., Kawakami, K., Mochizuki, A., Nagata, T., Suzuki, M., Kanno, H., Takemura, M., Ohta, T.

(2011) Bioorg Med Chem Lett 21: 2133-2140

• PubMed: 21345673 
• DOI: https://doi.org/10.1016/j.bmcl.2011.01.132
• Primary Citation Related Structures: 
  3Q3K


• PubMed Abstract: 
  

  We previously reported on a series of cyclohexanediamine derivatives as highly potent factor Xa inhibitors. Herein, we describe the modification of the spacer moiety to discover an alternative scaffold. Ethylenediamine derivatives possessing a substituent at the C1 position in S configuration and phenylenediamine derivatives possessing a substituent at the C5 position demonstrated moderate to strong anti-fXa activity. Further SAR studies led to the identification of compound 30 h which showed both good in vitro activity (fXa IC(50) = 2.2 nM, PTCT2 = 3.9 μM) and in vivo antithrombotic efficacy.

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Organizational Affiliation: 
• R&D Division, Daiichi Sankyo Co, Ltd, 1-16-13, Kita-Kasai, 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: 32.74 kDa 
• Atom Count: 2,275 
• Modeled Residue Count: 285 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activated factor Xa 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
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
D90	E [auth A]	N-(2-{[(5-chloro-1H-indol-2-yl)carbonyl]amino}phenyl)-5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridine-2-carboxamide C23 H20 Cl N5 O2 S HLZHKMHNSZRIOD-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: 2.00 Å
• R-Value Free:  0.216 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.073	α = 90
b = 73.202	β = 90
c = 79.52	γ = 90

Software Package:

Software Name	Purpose
specificary	data collection
REFMAC	refinement
PROCESS	data reduction
PROCESS	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Suzuki, M., Imai, E.

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2012-06-20
  Changes: Structure summary
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary