2Y5H

FACTOR XA - CATION INHIBITOR COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

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Literature

Molecular Recognition at the Active Site of Factor Xa: Cation-Pi Interactions, Stacking on Planar Peptide Surfaces, and Replacement of Structural Water.

Salonen, L.M., Holland, M.C., Kaib, P.S., Haap, W., Benz, J., Mary, J.L., Kuster, O., Schweizer, W.B., Banner, D.W., Diederich, F.

(2012) Chemistry 18: 213

  • DOI: https://doi.org/10.1002/chem.201102571
  • Primary Citation of Related Structures:  
    2Y5F, 2Y5G, 2Y5H

  • PubMed Abstract: 

    • Factor Xa, a serine protease from the blood coagulation cascade, is an ideal enzyme for molecular recognition studies, as its active site is highly shape-persistent and features distinct, concave sub-pockets. We developed a family of non-peptidic, small-molecule inhibitors with a central tricyclic core orienting a neutral heterocyclic substituent into the S1 pocket and a quaternary ammonium ion into the aromatic box in the S4 pocket ...

    Factor Xa, a serine protease from the blood coagulation cascade, is an ideal enzyme for molecular recognition studies, as its active site is highly shape-persistent and features distinct, concave sub-pockets. We developed a family of non-peptidic, small-molecule inhibitors with a central tricyclic core orienting a neutral heterocyclic substituent into the S1 pocket and a quaternary ammonium ion into the aromatic box in the S4 pocket. The substituents were systematically varied to investigate cation-π interactions in the S4 pocket, optimal heterocyclic stacking on the flat peptide walls lining the S1 pocket, and potential water replacements in both the S1 and the S4 pockets. Structure-activity relationships were established to reveal and quantify contributions to the binding free enthalpy, resulting from single-atom replacements or positional changes in the ligands. A series of high-affinity ligands with inhibitory constants down to K(i)=2 nM were obtained and their proposed binding geometries confirmed by X-ray co-crystal structures of protein-ligand complexes.

    Organizational Affiliation: 

    Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, HCI, 8093 Zürich, Switzerland.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACTIVATED FACTOR XA HEAVY CHAIN234Homo sapiensMutation(s): 1 
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FACTOR X LIGHT CHAINB [auth L]54Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y5H
Query on Y5H
Download Ideal Coordinates CCD File 
C [auth A]3-[(3AS,4R,5S,8AS,8BR)-4-[2-(5-CHLOROTHIOPHEN-2-YL)-1,3-OXAZOL-4-YL]-1,3-DIOXO-4,6,7,8,8A,8B-HEXAHYDRO-3AH-PYRROLO[3,4-A]PYRROLIZIN-2-YL]PROPYL-TRIMETHYL-AZANIUM
C22 H28 Cl N4 O3 S
JCNHSXPHCSYYCR-QZHFEQFPSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
Y5H PDBBind:  2Y5H Ki: 1620 (nM) from 1 assay(s)
Binding MOAD:  2Y5H Ki: 1620 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.888α = 90
b = 74.644β = 90
c = 77.082γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-01-18
    Changes: Other