7SFI | pdb_00007sfi

SARS-CoV-2 Main Protease (Mpro) in Complex with ML104

PDB DOI: https://doi.org/10.2210/pdb7SFI/pdb

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

Deposited: 2021-10-03 Released: 2022-10-05
Deposition Author(s): Westberg, M., Fernandez, D., Lin, M.Z.
Funding Organization(s): Novo Nordisk Foundation, Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.239 (Depositor), 0.214 (DCC)
R-Value Work:
0.195 (Depositor)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases

Westberg, M., Su, Y., Zou, X., Rustagi, A., Beck, A., Ning, L., Fernandez, D., Blish, C., Lin, M.Z.

To be published.

Macromolecule Content

Total Structure Weight: 34.43 kDa
Atom Count: 2,630
Modeled Residue Count: 306
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
91Z (Subject of Investigation/LOI) Query on 91Z Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(1R,2S,5S)-N-{(2S,3R)-4-amino-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-6,6-dimethyl-3-[N-(2,4,6-trifluorophenyl)glycyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide C₂₄ H₃₀ F₃ N₅ O₅ YNUIIZLFVOREIR-NZIQIWATSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.239 (Depositor), 0.214 (DCC)
R-Value Work: 0.195 (Depositor)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.49	α = 90
b = 63.586	β = 90
c = 105.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Novo Nordisk Foundation		NNF18OC0031816
Other private		--

Revision History (Full details and data files)

Version 1.0: 2022-10-05
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.