2WYJ | pdb_00002wyj

Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with monoaryl P4 motifs

• PDB DOI: https://doi.org/10.2210/pdb2WYJ/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2009-11-16 Released: 2010-12-01 
• Deposition Author(s): Kleanthous, S., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chaudry, L., Chan, C., Clarte, M., Convery, M.A., Harling, J.D., Hortense, E., Irving, W.R., Irvine, S., Pateman, A.J., Patikis, A., Pinto, I.L., Pollard, D.R., Roethka, T.J., Senger, S., Shah, G.P., Stelman, G.J., Toomey, J.R., Watson, N.S., Whittaker, C., Zhou, P., Young, R.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.255 (Depositor) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Monoaryl P4 Motifs

Kleanthous, S., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chaudry, L., Chan, C., Clarte, M., Convery, M.A., Harling, J.D., Hortense, E., Irving, W.R., Irvine, S., Pateman, A.J., Patikis, A., Pinto, I.L., Pollard, D.R., Roethka, T.J., Senger, S., Shah, G.P., Stelman, G.J., Toomey, J.R., Watson, N.S., Whittaker, C., Zhou, P., Young, R.J.

(2010) Bioorg Med Chem Lett 20: 618

• PubMed: 20006499 
• DOI: https://doi.org/10.1016/j.bmcl.2009.11.077
• Primary Citation Related Structures: 
  2WYG, 2WYJ


• PubMed Abstract: 
  

  Structure and property based drug design was exploited in the synthesis of sulfonamidopyrrolidin-2-one-based factor Xa inhibitors, incorporating neutral and basic monoaryl P4 groups, ultimately producing potent inhibitors with effective levels of anticoagulant activity and extended oral pharmacokinetic profiles. However, time dependant inhibition of Cytochrome P450 3A4 was a particular issue with this series.

---

Organizational Affiliation: 
• GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom.

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: 44.23 kDa 
• Atom Count: 2,332 
• Modeled Residue Count: 282 
• Deposited Residue Count: 388 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIVATED FACTOR XA HEAVY CHAIN	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
FACTOR X LIGHT CHAIN	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
898	C [auth A]	(E)-2-(5-CHLOROTHIOPHEN-2-YL)-N-[(3S)-1-{4-[(1S)-1-(DIMETHYLAMINO)ETHYL]-2-FLUOROPHENYL}-2-OXOPYRROLIDIN-3-YL]ETHENESULFONAMIDE C20 H23 Cl F N3 O3 S2 AFDHTIFDRFSZDA-WZMLOTFKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
898	BindingDB:  2WYJ	Ki: min: 0.8, max: 1 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.255 (Depositor) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.564	α = 90
b = 72.485	β = 90
c = 78.177	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-01 
Deposition Author(s): Kleanthous, S., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chaudry, L., Chan, C., Clarte, M., Convery, M.A., Harling, J.D., Hortense, E., Irving, W.R., Irvine, S., Pateman, A.J., Patikis, A., Pinto, I.L., Pollard, D.R., Roethka, T.J., Senger, S., Shah, G.P., Stelman, G.J., Toomey, J.R., Watson, N.S., Whittaker, C., Zhou, P., Young, R.J.

Revision History  

• Version 1.0: 2010-12-01
  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: 2019-05-29
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary