9DU2 | pdb_00009du2

SARS-CoV-2 Mpro in complex with compound 7

PDB DOI: https://doi.org/10.2210/pdb9DU2/pdb

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

Deposited: 2024-10-02 Released: 2025-04-30
Deposition Author(s): Bigelow, L., Tang, H., Boguslaw, N., Duda, D.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 ?
R-Value Free:
0.206 (Depositor), 0.208 (DCC)
R-Value Work:
0.161 (Depositor), 0.163 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Inhibition of Dimeric SARS-CoV-2 Mpro by Aldehyde and Nitrilebased Inhibitors Displays Positive Cooperativity and a Mixture of Covalent and Non-covalent Binding.

Padmanabha Das, K.M., Chen, J., Charifson, P.S., Green, J., Tang, H., Panchal, S., Pu, F., Korepanova, A., Afanador, G., Stojkovic, V., Nocek, B., Bigelow, L., Stubbs, S., Davey, R.A., DeGoey, D.A., Arthanari, H., Namchuk, M.N.

To be published.

Macromolecule Content

Total Structure Weight: 70.95 kDa
Atom Count: 5,035
Modelled Residue Count: 602
Deposited Residue Count: 630
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	315	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BCY (Subject of Investigation/LOI) Query on A1BCY Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	N-[(2S)-3-cyclopropyl-1-{[(1Z,2S)-1-imino-4-(methanesulfonyl)butan-2-yl]amino}-1-oxopropan-2-yl]-4-methoxy-1H-indole-2-carboxamide C₂₁ H₂₈ N₄ O₅ S ULZDIEQSFFSWTK-RWPQHDDLSA-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: 1.86 ?
R-Value Free: 0.206 (Depositor), 0.208 (DCC)
R-Value Work: 0.161 (Depositor), 0.163 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 55.068	α = 90
b = 98.956	β = 107.505
c = 59.102	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-04-30
Type: Initial release

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.