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)

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L-ABLE	B	126	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GG2 (Subject of Investigation/LOI) Query on GG2 Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-29

Deposition Author(s):

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 (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.