2UWP | pdb_00002uwp

Factor Xa inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb2UWP/pdb

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


• Deposited: 2007-03-22 Released: 2007-05-08 
• Deposition Author(s): Young, R.J., Brown, D., Burns-Kurtis, C.L., Chan, C., Convery, M.A., Hubbard, J.A., Kelly, H.A., Pateman, A.J., Patikis, A., Senger, S., Shah, G.P., Toomey, J.R., Watson, N.S., Zhou, P., Thorpe, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.212 (Depositor) 
• R-Value Work: 
  0.185 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Selective and Dual Action Orally Active Inhibitors of Thrombin and Factor Xa.

Young, R.J., Brown, D., Burns-Kurtis, C.L., Chan, C., Convery, M.A., Hubbard, J.A., Kelly, H.A., Pateman, A.J., Patikis, A., Senger, S., Shah, G.P., Toomey, J.R., Watson, N.S., Zhou, P.

(2007) Bioorg Med Chem Lett 17: 2927

• PubMed: 17420122 
• DOI: https://doi.org/10.1016/j.bmcl.2007.03.080
• Primary Citation Related Structures: 
  2UWL, 2UWO, 2UWP


• PubMed Abstract: 
  

  The synthetic entry to new classes of dual fXa/thrombin and selective thrombin inhibitors with significant oral bioavailability is described. This was achieved through minor modifications to the sulfonamide group in our potent and selective fXa inhibitor (E)-2-(5-chlorothien-2-yl)-N-{(3S)-1-[(1S)-1-methyl-2-(morpholin-4-yl)-2-oxoethyl]-2-oxopyrrolidin-3-yl}ethenesulfonamide and these observed activity changes have been rationalised using structural studies.

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Organizational Affiliation: 
• GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 44.28 kDa 
• Atom Count: 2,507 
• Modeled Residue Count: 287 
• Deposited Residue Count: 388 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X	A	254	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	B	134	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
894	C [auth A]	2-(5-CHLORO-2-THIENYL)-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}ETHANESULFONAMIDE C17 H24 Cl N3 O5 S2 IAUZEBLXCOCAFL-JSGCOSHPSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.212 (Depositor) 
• R-Value Work:  0.185 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.448	α = 90
b = 71.963	β = 90
c = 78.671	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-08 
Deposition Author(s): Young, R.J., Brown, D., Burns-Kurtis, C.L., Chan, C., Convery, M.A., Hubbard, J.A., Kelly, H.A., Pateman, A.J., Patikis, A., Senger, S., Shah, G.P., Toomey, J.R., Watson, N.S., Zhou, P., Thorpe, J.H.

Revision History  

• Version 1.0: 2007-05-08
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary