5VOE

DesGla-XaS195A Bound to Aptamer 11F7t


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass.

Gunaratne, R.Kumar, S.Frederiksen, J.W.Stayrook, S.Lohrmann, J.L.Perry, K.Bompiani, K.M.Chabata, C.V.Thalji, N.K.Ho, M.D.Arepally, G.Camire, R.M.Krishnaswamy, S.Sullenger, B.A.

(2018) Nat. Biotechnol. 36: 606-613

  • DOI: 10.1038/nbt.4153
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Unfractionated heparin (UFH), the standard anticoagulant for cardiopulmonary bypass (CPB) surgery, carries a risk of post-operative bleeding and is potentially harmful in patients with heparin-induced thrombocytopenia-associated antibodies. To improv ...

    Unfractionated heparin (UFH), the standard anticoagulant for cardiopulmonary bypass (CPB) surgery, carries a risk of post-operative bleeding and is potentially harmful in patients with heparin-induced thrombocytopenia-associated antibodies. To improve the activity of an alternative anticoagulant, the RNA aptamer 11F7t, we solved X-ray crystal structures of the aptamer bound to factor Xa (FXa). The finding that 11F7t did not bind the catalytic site suggested that it could complement small-molecule FXa inhibitors. We demonstrate that combinations of 11F7t and catalytic-site FXa inhibitors enhance anticoagulation in purified reaction mixtures and plasma. Aptamer-drug combinations prevented clot formation as effectively as UFH in human blood circulated in an extracorporeal oxygenator circuit that mimicked CPB, while avoiding side effects of UFH. An antidote could promptly neutralize the anticoagulant effects of both FXa inhibitors. Our results suggest that drugs and aptamers with shared targets can be combined to exert more specific and potent effects than either agent alone.


    Organizational Affiliation

    Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X
H
233Homo sapiensMutation(s): 1 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X
L
51Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Entity ID: 3
MoleculeChainsLengthOrganism
Aptamer 11F7t (36-MER)A36synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CFL
Query on CFL
A
DNA LINKINGC9 H13 F N3 O7 PDC
UFT
Query on UFT
A
DNA LINKINGC9 H12 F N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 55.916α = 90.00
b = 164.596β = 90.00
c = 124.646γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited StatesHL-074124
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited StatesHL-125422

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-07-18
    Type: Data collection, Database references