8JH6 | pdb_00008jh6

Crystal structure of apixaban-bound racemic ABLE

• PDB DOI: https://doi.org/10.2210/pdb8JH6/pdb

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


• Deposited: 2023-05-22 Released: 2024-05-29 
• Deposition Author(s): Zhao, K., Li, T.
• Funding Organization(s): Other private, Other government, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

Rapid clearance of achiral small-molecule drugs using de novo-designed proteins and their cyclic and mirror-image variants

Zhao, K., Li, T.

(2025) Nat Biomed Eng 

• DOI: https://doi.org/10.1038/s41551-025-01404-w

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 28.54 kDa 
• Atom Count: 2,285 
• Modeled Residue Count: 252 
• Deposited Residue Count: 252 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ABLE	A	126	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L-ABLE	B	126	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

Modified Residues  16 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL	A	D-PEPTIDE LINKING	C3 H7 N O2		--
DAR	A	D-PEPTIDE LINKING	C6 H15 N4 O2		--
DAS	A	D-PEPTIDE LINKING	C4 H7 N O4		--
DGL	A	D-PEPTIDE LINKING	C5 H9 N O4		--
DGN	A	D-PEPTIDE LINKING	C5 H10 N2 O3		--
DHI	A	D-PEPTIDE LINKING	C6 H10 N3 O2		--
DIL	A	D-PEPTIDE LINKING	C6 H13 N O2		--
DLE	A	D-PEPTIDE LINKING	C6 H13 N O2		--
DLY	A	D-PEPTIDE LINKING	C6 H14 N2 O2		--
DPN	A	D-PEPTIDE LINKING	C9 H11 N O2		--
DSG	A	D-PEPTIDE LINKING	C4 H8 N2 O3		--
DSN	A	D-PEPTIDE LINKING	C3 H7 N O3		--
DTH	A	D-PEPTIDE LINKING	C4 H9 N O3		--
DTY	A	D-PEPTIDE LINKING	C9 H11 N O3		--
DVA	A	D-PEPTIDE LINKING	C5 H11 N O2		--
MED	A	D-PEPTIDE LINKING	C5 H11 N O2 S		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.362	α = 90.53
b = 42.483	β = 97.91
c = 43.994	γ = 110.83

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
PHASER	phasing
CrysalisPro	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Zhao, K., Li, T.

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Funding Organization	Location	Grant Number
Other private	China	32120103013
Other government	China	No. 2021C03040
National Natural Science Foundation of China (NSFC)	China	22077104

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary
• Version 1.2: 2025-06-04
  Changes: Database references