2Y7X | pdb_00002y7x

The discovery of potent and long-acting oral factor Xa inhibitors with tetrahydroisoquinoline and benzazepine P4 motifs

• PDB DOI: https://doi.org/10.2210/pdb2Y7X/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.230 (Depositor) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

The Discovery of Potent and Long-Acting Oral Factor Xa Inhibitors with Tetrahydroisoquinoline and Benzazepine P4 Motifs.

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

(2011) Bioorg Med Chem Lett 21: 1588

• PubMed: 21349711 
• DOI: https://doi.org/10.1016/j.bmcl.2011.01.129
• Primary Citation Related Structures: 
  2Y7X


• PubMed Abstract: 
  

  The discovery and evaluation of potent and long-acting oral sulfonamidopyrrolidin-2-one factor Xa inhibitors with tetrahydroisoquinoline and benzazepine P4 motifs are described. Unexpected selectivity issues versus tissue plasminogen activator in the former series were addressed in the later, delivering a robust candidate for progression towards clinical studies.

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Organizational Affiliation: 
• GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, 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: 44.3 kDa 
• Atom Count: 2,508 
• Modeled Residue Count: 288 
• 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
MZA	C [auth A]	6-CHLORO-N-[(3S)-1-(5-FLUORO-1,2,3,4-TETRAHYDROISOQUINOLIN-6-YL)-2-OXO-PYRROLIDIN-3-YL]NAPHTHALENE-2-SULFONAMIDE C23 H21 Cl F N3 O3 S BJOZEZZETKKCMQ-FQEVSTJZSA-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
MZA	BindingDB:  2Y7X	Ki: 1.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.230 (Depositor) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.859	α = 90
b = 71.599	β = 90
c = 78.279	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

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

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: 2017-06-28
  Changes: Data collection
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary