2Y81 | pdb_00002y81

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

• PDB DOI: https://doi.org/10.2210/pdb2Y81/pdb

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


• Deposited: 2011-02-02 Released: 2011-03-16 
• Deposition Author(s): Young, R.J., Adams, C., Blows, M., Brown, D., Burns-Kurtis, C.L., Chaudry, L., Chan, C., Convery, M.A., Davies, D.E., Exall, A.M., Foster, G., Harling, J.D., Hortense, E., Irving, W.R., Irvine, S., Jackson, S., Kleanthous, S., Pateman, A.J., Patikis, A.N., Roethka, T.J., Senger, S., Stelman, G.J., Toomey, J.R., West, R.I., Whittaker, C., Zhou, P., Watson, N.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.225 (Depositor) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

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

Young, R.J., Adams, C., Blows, M., Brown, D., Burns-Kurtis, C.L., Chan, C., Chaudry, L., Convery, M.A., Davies, D.E., Exall, A.M., Foster, G., Harling, J.D., Hortense, E., Irvine, S., Irving, W.R., Jackson, S., Kleanthous, S., Pateman, A.J., Patikis, A.N., Roethka, T.J., Senger, S., Stelman, G.J., Toomey, J.R., West, R.I., Whittaker, C., Zhou, P., Watson, N.S.

(2011) Bioorg Med Chem Lett 21: 1582

• PubMed: 21349710 
• DOI: https://doi.org/10.1016/j.bmcl.2011.01.131
• Primary Citation Related Structures: 
  2Y7Z, 2Y80, 2Y81, 2Y82


• PubMed Abstract: 
  

  The rational design, syntheses and evaluation of potent sulfonamidopyrrolidin-2-one-based factor Xa inhibitors incorporating aminoindane and phenylpyrrolidine P4 motifs are described. These series delivered highly potent anticoagulant compounds with excellent oral pharmacokinetic profiles; however, significant time dependant P450 inhibition was an issue for the aminoindane series, but this was not observed with the phenylpyrrolidine motif, which produced candidate quality molecules with potential for once-daily oral dosing in humans.

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Organizational Affiliation: 
• GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, United Kingdom. [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: 44.31 kDa 
• Atom Count: 2,530 
• Modeled Residue Count: 286 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
931	C [auth A]	6-CHLORO-N-((3S)-2-OXO-1-{4-[(2R)-2--PYRROLIDINYL] PHENYL}-3-PYRROLIDINYL)-2-NAPHTHALENESULFONAMIDE C24 H23 Cl F N3 O3 S OKMBULRSJZKGQF-YADHBBJMSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
931	BindingDB:  2Y81	Ki: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.225 (Depositor) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.665	α = 90
b = 72.033	β = 90
c = 78.151	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Young, R.J., Adams, C., Blows, M., Brown, D., Burns-Kurtis, C.L., Chaudry, L., Chan, C., Convery, M.A., Davies, D.E., Exall, A.M., Foster, G., Harling, J.D., Hortense, E., Irving, W.R., Irvine, S., Jackson, S., Kleanthous, S., Pateman, A.J., Patikis, A.N., Roethka, T.J., Senger, S., Stelman, G.J., Toomey, J.R., West, R.I., Whittaker, C., Zhou, P., Watson, N.S.

Revision History  

• Version 1.0: 2011-03-16
  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: 2019-10-16
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary