4JN1 | pdb_00004jn1

An Antidote for Dabigatran

• PDB DOI: https://doi.org/10.2210/pdb4JN1/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2013-03-14 Released: 2013-03-27 
• Deposition Author(s): Schiele, F., Nar, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.197 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

A specific antidote for dabigatran: functional and structural characterization.

Schiele, F., van Ryn, J., Canada, K., Newsome, C., Sepulveda, E., Park, J., Nar, H., Litzenburger, T.

(2013) Blood 121: 3554-3562

• PubMed: 23476049 
• DOI: https://doi.org/10.1182/blood-2012-11-468207
• Primary Citation Related Structures: 
  4JN1, 4JN2


• PubMed Abstract: 
  

  Dabigatran etexilate is a direct thrombin inhibitor and used widely as an anticoagulant for the prevention of stroke in patients with atrial fibrillation. However, anticoagulation therapy can be associated with an increased risk of bleeding. Here, we present data on the identification, humanization, and in vitro pharmacology of an antidote for dabigatran (aDabi-Fab). The X-ray crystal structure of dabigatran in complex with the antidote reveals many structural similarities of dabigatran recognition compared with thrombin. By a tighter network of interactions, the antidote achieves an affinity for dabigatran that is ~350 times stronger than its affinity for thrombin. Despite the structural similarities in the mode of dabigatran binding, the antidote does not bind known thrombin substrates and has no activity in coagulation tests or platelet aggregation. In addition we demonstrate that the antidote rapidly reversed the anticoagulant activity of dabigatran in vivo in a rat model of anticoagulation. This is the first report of a specific antidote for a next-generation anticoagulant that may become a valuable tool in patients who require emergency procedures.

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Organizational Affiliation: 
• Structural Research Group, Boehringer Ingelheim GmbH & Co. KG, Biberach, Germany.

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: 48.57 kDa 
• Atom Count: 3,820 
• Modeled Residue Count: 444 
• Deposited Residue Count: 444 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-dabigatran Fab1, heavy chain	A [auth H]	225	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-dabigatran Fab1, light chain	B [auth L]	219	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth H], D [auth H], E [auth H], F [auth H], G [auth H], H, I [auth L], J [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.197 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.132	α = 90
b = 78.217	β = 89.91
c = 63.434	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Schiele, F., Nar, H.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2013-07-24
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary