2PHB

An Orally Efficacious Factor Xa Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2PHB/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-10 Released: 2008-03-25 
• Deposition Author(s): Zhang, E., Kohrt, J.T., Bigge, C.F., Finzel, B.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.296 
• R-Value Work: 0.260 

Literature

The discovery of (2R,4R)-N-(4-chlorophenyl)-N- (2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl)-4-methoxypyrrolidine-1,2-dicarboxamide (PD 0348292), an orally efficacious factor Xa inhibitor

Kohrt, J.T., Bigge, C.F., Bryant, J.W., Casimiro-Garcia, A., Chi, L., Cody, W.L., Dahring, T., Dudley, D.A., Filipski, K.J., Haarer, S., Heemstra, R., Janiczek, N., Narasimhan, L., McClanahan, T., Peterson, J.T., Sahasrabudhe, V., Schaum, R., Van Huis, C.A., Welch, K.M., Zhang, E., Leadley, R.J., Edmunds, J.J.

(2007) Chem Biol Drug Des 70: 100-112

• PubMed: 17683371 
• DOI: https://doi.org/10.1111/j.1747-0285.2007.00539.x
• Primary Citation of Related Structures:  
  2PHB


• PubMed Abstract: 
  

  Herein, we report the discovery of novel, proline-based factor Xa inhibitors containing a neutral P1 chlorophenyl pharmacophore. Through the additional incorporation of 1-(4-amino-3-fluoro-phenyl)-1H-pyridin-2-one 22, as a P4 pharmacophore, we discovered compound 7 (PD 0348292). This compound is a selective, orally bioavailable, efficacious FXa inhibitor that is currently in phase II clinical trials for the treatment and prevention of thrombotic disorders.

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Organizational Affiliation: 

Michigan Laboratories, Ann Arbor Campus, Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. [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: 32.43 kDa 
• Atom Count: 2,314 
• Modelled Residue Count: 285 
• Deposited Residue Count: 285 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X, heavy chain	A	234	Homo sapiens	Mutation(s): 0  Gene Names: F10 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	51	Homo sapiens	Mutation(s): 0  Gene Names: F10 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
230	D [auth A]	(2R,4R)-N~1~-(4-CHLOROPHENYL)-N~2~-[2-FLUORO-4-(2-OXOPYRIDIN-1(2H)-YL)PHENYL]-4-METHOXYPYRROLIDINE-1,2-DICARBOXAMIDE C24 H22 Cl F N4 O4 QQBKAVAGLMGMHI-WIYYLYMNSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
230	PDBBind:  2PHB	Kd: 0.32 (nM) from 1 assay(s)
	BindingDB:  2PHB	IC50: min: 0.32, max: 0.57 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.296 
• R-Value Work: 0.260 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.483	α = 90
b = 72.406	β = 90
c = 77.715	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Zhang, E., Kohrt, J.T., Bigge, C.F., Finzel, B.C.

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Advisory, Refinement description