6W70

Crystal Structure of apixaban-bound ABLE

PDB DOI: https://doi.org/10.2210/pdb6W70/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-03-18 Released: 2020-08-26
Deposition Author(s): Polizzi, N.F.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.183
R-Value Work: 0.161
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

A defined structural unit enables de novo design of small-molecule-binding proteins.

Polizzi, N.F., DeGrado, W.F.

(2020) Science 369: 1227-1233

PubMed: 32883865 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.abb8330
Primary Citation of Related Structures:
6W6X, 6W70, 6X8N

PubMed Abstract:
The de novo design of proteins that bind highly functionalized small molecules represents a great challenge. To enable computational design of binders, we developed a unit of protein structure-a van der Mer (vdM)-that maps the backbone of each amino acid to statistically preferred positions of interacting chemical groups. Using vdMs, we designed six de novo proteins to bind the drug apixaban; two bound with low and submicromolar affinity. X-ray crystallography and mutagenesis confirmed a structure with a precisely designed cavity that forms favorable interactions in the drug-protein complex. vdMs may enable design of functional proteins for applications in sensing, medicine, and catalysis.

Organizational Affiliation

Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA. nicholas.polizzi@ucsf.edu william.degrado@ucsf.edu.

Macromolecule Content

Total Structure Weight: 28.77 kDa
Atom Count: 2,259
Modelled Residue Count: 252
Deposited Residue Count: 252
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed ABLE	A, B [auth C]	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 3 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 E [auth A] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C]	E [auth A], G [auth C]	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 E [auth A] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A]	D [auth A], F [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A]