8VFQ | pdb_00008vfq

De novo design apixaban-binding protein: apx1049

• PDB DOI: https://doi.org/10.2210/pdb8VFQ/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-21 Released: 2024-12-25 
• Deposition Author(s): Bera, A.K., Lee, G.R., Baker, D.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA), Howard Hughes Medical Institute (HHMI), Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.323 (Depositor), 0.323 (DCC) 
• R-Value Work: 
  0.279 (Depositor), 0.279 (DCC) 
• R-Value Observed: 
  0.284 (Depositor) 

Starting Model: other

Literature

Small-molecule binding and sensing with a designed protein family.

Lee, G.R., Pellock, S.J., Norn, C., Tischer, D., Dauparas, J., Anishchenko, I., Mercer, J.A.M., Kang, A., Bera, A.K., Nguyen, H., Brackenbrough, E., Sankaran, B., Goreshnik, I., Vafeados, D., Roullier, N., Han, H.L., Coventry, B., Haddox, H.K., Liu, D.R., Yeh, A.H., Baker, D.

(2026) Nat Commun 17

• PubMed: 41904144 
• DOI: https://doi.org/10.1038/s41467-026-70953-8
• Primary Citation Related Structures: 
  8UQF, 8VEZ, 8VFQ


• PubMed Abstract: 
  

  The de novo design of small-molecule-binding proteins holds great promise as a potential tool to develop sensors on-demand for arbitrary small molecules. Here we combine deep learning and physics-based methods to generate a family of proteins with diverse and designable pocket geometries, which we employ to computationally design binders for six small-molecule targets. Biophysical characterization of the designed binders reveals nanomolar to low micromolar binding affinities and atomic-level design accuracy. Additionally, we use a cortisol binder to design a chemically induced dimerization (CID) system that enables the construction of a biosensor for cortisol detection. The approach described here demonstrates the potential of the NTF2 fold and deep learning-based protein design in sensor development, paving the way for future platforms to design binders and sensors for small molecules across analytical, environmental, and biomedical applications.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA.
Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, 1 Cyclotron Road, Berkeley, CA, USA.
Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.83 kDa 
• Atom Count: 1,919 
• Modeled Residue Count: 225 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed apixaban-binding protein apx1049	A, B	117	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GG2 (Subject of Investigation/LOI)	C [auth A], D [auth B]	1-(4-METHOXYPHENYL)-7-OXO-6-[4-(2-OXOPIPERIDIN-1-YL)PHENYL]-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3,4-C]PYRIDINE-3-CARBOXAMIDE C25 H25 N5 O4 QNZCBYKSOIHPEH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.323 (Depositor), 0.323 (DCC) 
• R-Value Work:  0.279 (Depositor), 0.279 (DCC) 
• R-Value Observed: 0.284 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.47	α = 90
b = 60.271	β = 90
c = 63.277	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Bera, A.K., Lee, G.R., Baker, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	--
Howard Hughes Medical Institute (HHMI)	United States	--
Department of Defense (DOD, United States)	United States	--

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release
  
• Version 1.1: 2026-07-08
  Changes: Database references