9IK2

The co-crystal structure of SARS-CoV-2 Mpro in complex with compound H109

PDB DOI: https://doi.org/10.2210/pdb9IK2/pdb

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

Deposited: 2024-06-26 Released: 2024-07-31
Deposition Author(s): Feng, Y., Zheng, W.Y., Han, P., Fu, L.F., Qi, J.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.212
R-Value Work: 0.183
R-Value Observed: 0.185

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

Structure-guided discovery of a small molecule inhibitor of SARS-CoV-2 main protease with potent in vitro and in vivo antiviral activities

Yuan, S.F., Wang, J., Sang, X.H., Xie, Y.B., Feng, Y., Poon, V., Chan, C., Tsang, J.O., Chik, K., Zhou, J., Xu, Y., Han, P., Zheng, W.Y., Fu, L.F., Huang, L.S.M., Wu, M.X., An, J., Yuen, K.Y., Qi, J.X., Huang, Z.W., Chan, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 34.34 kDa
Atom Count: 2,612
Modelled Residue Count: 304
Deposited Residue Count: 306
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	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1 Go to UniProtKB: P0DTC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D9H (Subject of Investigation/LOI) Query on A1D9H Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	tert-butyl N-[(2S)-1-[[(2S)-1-[[(2S)-1-azanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate C₂₇ H₄₁ N₅ O₅ YWXGXHNDBCVDDN-NFIWZKORSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.212
R-Value Work: 0.183
R-Value Observed: 0.185
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.223	α = 90
b = 106.223	β = 90
c = 82.382	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
Coot	model building
PHENIX	refinement
PHASES	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	92169208

Revision History (Full details and data files)

Version 1.0: 2024-07-31
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 R01GM133198.