Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 32.59 kDa 
• Atom Count: 2395 
• Residue Count: 286 
• Unique protein chains: 2

3CS7

FACTOR XA IN COMPLEX WITH THE INHIBITOR 1-(4-methoxyphenyl)-6-(4-(1-(pyrrolidin-1-ylmethyl)cyclopropyl)phenyl)-3-(trifluoromethyl)-5,6-dihydro-1H-pyrazolo[3,4-c]pyridin-7(4H)-one

• DOI: 10.2210/pdb3CS7/pdb

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


• Deposited: 2008-04-09 Released: 2008-07-08 
• Deposition Author(s): Alexander, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.274 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Literature

Achieving structural diversity using the perpendicular conformation of alpha-substituted phenylcyclopropanes to mimic the bioactive conformation of ortho-substituted biphenyl P4 moieties: discovery of novel, highly potent inhibitors of Factor Xa.

Qiao, J.X., Cheney, D.L., Alexander, R.S., Smallwood, A.M., King, S.R., He, K., Rendina, A.R., Luettgen, J.M., Knabb, R.M., Wexler, R.R., Lam, P.Y.

(2008) Bioorg Med Chem Lett 18: 4118-4123

• PubMed: 18550370 
• DOI: 10.1016/j.bmcl.2008.05.095
• Primary Citation of Related Structures:  
  3CS7


• PubMed Abstract: 
  

Ortho-substituted biphenyl moieties are widely used in drug design. We herein report a successful use of the perpendicular conformation of the alpha-substituted phenylcyclopropyl groups to mimic the aplanar, biologically active conformation of the ortho-substituted biphenyl moieties to achieve structural diversity. This is exemplified by the design and synthesis of a series of highly potent pyrazole bicyclic-based Factor Xa (FXa) inhibitors bearing alpha-substituted phenylcyclopropyl P4 moieties. The designed perpendicular conformation was confirmed by the X-ray structure of FXa-bound compound 2r. The potential structural basis for the high FXa potency in the phenylcyclopropyl P4 analogs and their improved FXa inhibitory activities compared with the biphenyl P4 counterparts are discussed.

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Organizational Affiliation: 

Bristol-Myers Squibb Company, Research and Development, PO Box 5400, Princeton, NJ 08543-5400, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	A	234	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742 GTEx  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	L	52	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742 GTEx  ENSG00000126218

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LG0	A	1-(4-methoxyphenyl)-6-(4-(1-(pyrrolidin-1-ylmethyl)cyclopropyl)phenyl)-3-(trifluoromethyl)-5,6-dihydro-1H-pyrazolo[3,4-c]pyridin-7(4H)-one C28 H29 F3 N4 O2 VNHRSGCBTKUBAX-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LG0	Ki:  0.020999999716877937   nM  Binding MOAD
LG0	Ki :  0.021000001579523087   nM  PDBBind
LG0	Ki:  0.019999999552965164   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.274 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.5	α = 90
b = 72.6	β = 90
c = 79	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-09 
• Released Date: 2008-07-08 
Deposition Author(s): Alexander, R.S.

Revision History 

• Version 1.0: 2008-07-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance