4Y79

Factor Xa complex with GTC000406

• PDB DOI:  https://doi.org/10.2210/pdb4Y79/pdb

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


• Deposited: 2015-02-13 Released: 2015-09-30 
• Deposition Author(s): Convery, M.A., Young, R.J., Senger, S., Hamblin, J.N., Chan, C., Toomey, J.R., Watson, N.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.216 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Factor Xa inhibitors: S1 binding interactions of a series of N-{(3S)-1-[(1S)-1-methyl-2-morpholin-4-yl-2-oxoethyl]-2-oxopyrrolidin-3-yl}sulfonamides.

Chan, C., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chaudry, L., Chung, C.W., Convery, M.A., Hamblin, J.N., Johnstone, L., Kelly, H.A., Kleanthous, S., Patikis, A., Patel, C., Pateman, A.J., Senger, S., Shah, G.P., Toomey, J.R., Watson, N.S., Weston, H.E., Whitworth, C., Young, R.J., Zhou, P.

(2007) J Med Chem 50: 1546-1557

• PubMed: 17338508 
• DOI: https://doi.org/10.1021/jm060870c
• Primary Citation of Related Structures:  
  2J94, 2J95, 4Y76, 4Y79


• PubMed Abstract: 
  

Factor Xa inhibitory activities for a series of N-{(3S)-1-[(1S)-1-methyl-2-morpholin-4-yl-2-oxoethyl]-2-oxopyrrolidin-3-yl}sulfonamides with different P1 groups are described. These data provide insight into binding interactions within the S1 primary specificity pocket; rationales are presented for the derived SAR on the basis of electronic interactions through crystal structures of fXa-ligand complexes and molecular modeling studies. A good correlation between in vitro anticoagulant activities with lipophilicity and the extent of human serum albumin binding is observed within this series of potent fXa inhibitors. Pharmacokinetic profiles in rat and dog, together with selectivity over other trypsin-like serine proteases, identified 1f as a candidate for further evaluation.

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Organizational Affiliation: 

CVU UK Medicinal Chemistry Department, GlaxoSmithKline Research and Development, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, 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: 44.27 kDa 
• Atom Count: 2,518 
• Modelled 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  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	B	134	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4O6	E [auth A]	(E)-2-(4-chlorophenyl)-N-{(3S)-1-[(2S)-1-(morpholin-4-yl)-1-oxopropan-2-yl]-2-oxopyrrolidin-3-yl}ethenesulfonamide C19 H24 Cl N3 O5 S DNCVZNVETAOAJO-PPYZAHLJSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4O6	BindingDB:  4Y79	Ki: 11 (nM) from 1 assay(s)
	Binding MOAD:  4Y79	Ki: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.216 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.914	α = 90
b = 72.756	β = 90
c = 79.901	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Convery, M.A., Young, R.J., Senger, S., Hamblin, J.N., Chan, C., Toomey, J.R., Watson, N.S.

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release