2Y5F

FACTOR XA - CATION INHIBITOR COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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: 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACTIVATED FACTOR XA HEAVY CHAINA234Homo 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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XWG (Subject of Investigation/LOI)
Query on XWG

Download Ideal Coordinates CCD File 
C [auth A](3AS,4R,5S,8AS,8BR)-4-[5-(5-CHLOROTHIOPHEN-2-YL)-1,2-OXAZOL-3-YL]-2-[3-[1-(2-HYDROXYETHYL)PYRROLIDIN-1-IUM-1-YL]PROPYL]-4,6,7,8,8A,8B-HEXAHYDRO-3AH-PYRROLO[3,4-A]PYRROLIZINE-1,3-DIONE
C25 H32 Cl N4 O4 S
NGWQPUFWVMNLQW-ZMVGRULKSA-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
XWG Binding MOAD:  2Y5F Ki: 2 (nM) from 1 assay(s)
PDBBind:  2Y5F Ki: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.937α = 90
b = 74.3β = 90
c = 77.201γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment  



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