38LZ | pdb_000038lz

Crystal structure of SARS-CoV-2 (Covid-19) Nsp3 macrodomain in complex with compound 12p

• PDB DOI: https://doi.org/10.2210/pdb38LZ/pdb

• Classification: VIRAL PROTEIN, HYDROLASE/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2026-09-02 Released: 2026-09-23 
• Deposition Author(s): Wallace, S.D., Fromme, J.C.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Development of GS-441524 derivatives as potent SARS-CoV-2 Mac1 inhibitors via a direct-to-biology approach.

Peng, K., Chakraborty, S., Wallace, S.D., Noll, J.C.G., Shang, J., Lu, X., Choi, A., Whittaker, G., Fromme, J.C., Lin, H.

(2026) Eur J Med Chem 320: 119280-119280

• PubMed: 42721552 
• DOI: https://doi.org/10.1016/j.ejmech.2026.119280
• Primary Citation Related Structures: 
  38LZ


• PubMed Abstract: 
  

  Targeting viral macrodomains (Mac) has emerged as a promising strategy for antiviral drug development, especially after the outbreak of COVID-19 that claimed millions of lives worldwide. Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Mac1 inhibitors have been reported in the past few years. In the present work, we converted GS-441524 (IC ₅₀ of ∼10 μM for SARS-CoV-2 Mac1) to KP-S54 (18c), a potent inhibitor of both SARS-CoV-2 Mac1 (IC ₅₀ : 44 nM) and Middle East respiratory syndrome coronavirus (MERS-CoV) Mac1 (IC ₅₀ : 91 nM) through an iterative direct-to-biology approach. This approach leverages efficient amide-coupling reaction and the mix-and-read fluorescence polarization (FP) assays where reaction mixtures could be screened directly without purification. Cocrystal structure of a selected derivative (12p) binding to SARS-CoV-2 Mac1 revealed the binding mode, which will guide future drug development against viral macrodomains.

---

Organizational Affiliation: 
• Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA; Center for Chemical Biology and Therapeutics, The University of Chicago, Chicago, IL, 60637, USA; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.
Departments of Microbiology & Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA.
Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA; Center for Chemical Biology and Therapeutics, The University of Chicago, Chicago, IL, 60637, USA; Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA; Howard Hughes Medical Institute, Department of Medicine, Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.39 kDa 
• Atom Count: 2,972 
• Modeled Residue Count: 335 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B	170	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D4K (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-{2-[({(3aR,4R,6R,6aR)-6-[(8R)-4-aminopyrrolo[2,1-f][1,2,4]triazin-7-yl]-6-cyano-2,2-dimethyltetrahydro-2H-furo[3,4-d][1,3]dioxol-4-yl}methyl)amino]-2-oxoethyl}-5-(4-fluorobenzene-1-sulfonamido)pyridine-3-carboxamide C29 H28 F N9 O7 S FJWCRNZNSHWTLY-NFCHJMJDSA-N
A1D4L	E [auth B]	3,6,9,12,15,18,21,24,27,30-decaoxadotriacontane-1,32-diol C22 H46 O12 PSVXZQVXSXSQRO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.91	α = 90
b = 88.9	β = 94.879
c = 43.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-23 
Deposition Author(s): Wallace, S.D., Fromme, J.C.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1531632
National Science Foundation (NSF, United States)	United States	DMR-1829070
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM124166
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM136258

Revision History  

• Version 1.0: 2026-09-23
  Type: Initial release