38HC | pdb_000038hc

Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z9941018066

PDB DOI: https://doi.org/10.2210/pdb38HC/pdb

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

Deposited: 2026-08-26 Released: 2026-10-14
Deposition Author(s): Lyubimov, A.Y., Zielinski, K.A., Fraser, J.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free:
0.184 (Depositor), 0.184 (DCC)
R-Value Work:
0.156 (Depositor), 0.157 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

A Unified 3D Generative Model for Synthesizable Structure-Based Drug Design

Igashov, I., Schneuing, A., Dobbelstein, A.W., Morozova, I., Neeser, R., Zielinski, K.A., Abriata, L.A., Petruzzella, A.S., Iosub, D.R.P., Gampp, O., Lyubimov, A.Y., Elizarova, E., Ferrara, I., Sousa, P.M.F., Lemos, A.R., Testori, F., Herrera, P.A.M., Kanis, L., Schmidt, J., Braza, M.K.E., Amaro, R.E., Thoma, N., Ferraris, D.M., Riek, R., Fraser, J.S., Schwaller, P., Bronstein, M., Correia, B.

To be published.

Macromolecule Content

Total Structure Weight: 37.29 kDa
Atom Count: 3,185
Modeled Residue Count: 335
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B	169	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D0V (Subject of Investigation/LOI) Query on A1D0V Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-[(5M)-5-(3-methyl-1H-pyrazol-4-yl)pyridin-3-yl]benzenesulfonamide C₁₅ H₁₄ N₄ O₂ S CMSBUALLMDSFKA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	G [auth A], I [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B]	D [auth A], F [auth A], H [auth B], J [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B]