2PR3 | pdb_00002pr3

Factor XA inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2PR3/pdb

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


• Deposited: 2007-05-03 Released: 2007-08-14 
• 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: 1.50 Å
• R-Value Free: 
  0.267 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.249 (DCC) 

Literature

Structure-based drug design of pyrrolidine-1, 2-dicarboxamides as a novel series of orally bioavailable factor Xa inhibitors

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

(2007) Chem Biol Drug Des 69: 444-450

• PubMed: 17581239 
• DOI: https://doi.org/10.1111/j.1747-0285.2007.00520.x
• Primary Citation Related Structures: 
  2PR3


• PubMed Abstract: 
  

  A novel series of pyrrolidine-1,2-dicarboxamides was discovered as factor Xa inhibitors using structure-based drug design. This series consisted of a neutral 4-chlorophenylurea P1, a biphenylsulfonamide P4 and a D-proline scaffold (1, IC(50) = 18 nM). Optimization of the initial hit resulted in an orally bioavailable, subnanomolar inhibitor of factor Xa (13, IC(50) = 0.38 nM), which was shown to be efficacious in a canine electrolytic model of thrombosis with minimal bleeding.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 32.53 kDa 
• Atom Count: 2,482 
• Modeled Residue Count: 284 
• 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
237	E [auth A]	(2R,4R)-N~1~-(4-CHLOROPHENYL)-N~2~-[3-FLUORO-2'-(METHYLSULFONYL)BIPHENYL-4-YL]-4-METHOXYPYRROLIDINE-1,2-DICARBOXAMIDE C26 H25 Cl F N3 O5 S QBTQRXKLWHEJQY-AUSIDOKSSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.267 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.249 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.485	α = 90
b = 72.354	β = 90
c = 77.88	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Zhang, E., Kohrt, J.T., Bigge, C.F., Finzel, B.C.

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary