Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48517.11 
• Atom Count: 3403 
• Residue Count: 441 
• Unique protein chains: 2

4YHK

Reversal Agent for Dabigatran

• DOI: 10.2210/pdb4YHK/pdb

• Classification: IMMUNE SYSTEM
• Expression System: Cricetinae


• Deposited: 2015-02-27 Released: 2016-01-13 
• Deposition Author(s): Schiele, F., Nar, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.234 
• R-Value Work: 0.174 

Literature

Structure-guided residence time optimization of a dabigatran reversal agent.

Schiele, F., van Ryn, J., Litzenburger, T., Ritter, M., Seeliger, D., Nar, H.

(2015) Mabs 7: 871-880

• PubMed: 26047352 
• DOI: 10.1080/19420862.2015.1057364
• Primary Citation of Related Structures:  
  4YHO, 4YHN, 4YHM, 4YHL, 4YHI, 4YGV


• PubMed Abstract: 
  

Novel oral anticoagulants are effective and safe alternatives to vitamin-K antagonists for anticoagulation therapy. However, anticoagulation therapy in general is associated with an elevated risk of bleeding. Idarucizumab is a reversal agent for the direct thrombin inhibitor, dabigatran etexilate (Pradaxa®) and is currently in Phase 3 studies. Here, we report data on the antibody fragment aDabi-Fab2, a putative backup molecule for idarucizumab. Although aDabi-Fab2 completely reversed effects of dabigatran in a rat model in vivo, we observed significantly reduced duration of action compared to idarucizumab. Rational protein engineering, based on the X-ray structure of aDabi-Fab2, led to the identification of mutant Y103W. The mutant had optimized shape complementarity to dabigatran while maintaining an energetically favored hydrogen bond. It displayed increased affinity for dabigatran, mainly driven by a slower off-rate. Interestingly, the increased residence time translated into longer duration of action in vivo. It was thus possible to further enhance the efficacy of aDabi-Fab2 based on rational design, giving it the potential to serve as a back-up candidate for idarucizumab.

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Organizational Affiliation: 

a New Biological Entities Discovery; Boehringer Ingelheim GmbH & Co. KG ; Biberach , Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
aDabi-Fab2a heavy chain	H	222	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
aDabi-Fab2a light chain	L	219	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	H, L	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
4CC	H	N-[(2-{[(4-carbamimidoylphenyl)amino]methyl}-1-methyl-1H-benzimidazol-5-yl)carbonyl]-N-pyridin-2-yl-beta-alanine C25 H25 N7 O3 YBSJFWOBGCMAKL-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4CC	IC50: 4.6 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.234 
• R-Value Work: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 48.201	α = 90.00
b = 59.739	β = 90.00
c = 127.689	γ = 90.00

Software Package:

Software Name	Purpose
BUSTER-TNT	phasing
XDS	data scaling
BUSTER	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-02-27 
• Released Date: 2016-01-13 
• Deposition Author(s): Schiele, F., Nar, H.

Revision History 

• Version 1.0: 2016-01-13
  Type: Initial release