9L13 | pdb_00009l13

The crystal structure of SARS-CoV-2 Main protease in complex with an iso-quinoline-derived inhibitor FD6-31

PDB DOI: https://doi.org/10.2210/pdb9L13/pdb

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

Deposited: 2024-12-13 Released: 2025-12-17
Deposition Author(s): Zhong, B.S., Luo, G., Wang, G., Lu, W.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.233 (Depositor), 0.237 (DCC)
R-Value Work:
0.198 (Depositor), 0.214 (DCC)
R-Value Observed:
0.199 (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

The crystal structure of SARS-CoV-2 Main protease in complex with an iso-quinoline-derived inhibitor FD6-31

Zhong, B.S., Luo, G., Wang, G., Lu, W.Y.

To be published.

Macromolecule Content

Total Structure Weight: 33.67 kDa
Atom Count: 2,379
Modeled Residue Count: 301
Deposited Residue Count: 301
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	301	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
A1EH0 (Subject of Investigation/LOI) Query on A1EH0 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]	(5-chloranylspiro[1~{H}-2-benzofuran-3,4'-piperidine]-1'-yl)-isoquinolin-4-yl-methanone C₂₂ H₁₉ Cl N₂ O₂ RJTPGFSJXJKVJI-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.233 (Depositor), 0.237 (DCC)
R-Value Work: 0.198 (Depositor), 0.214 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.15	α = 90
b = 80.9	β = 114.67
c = 51.55	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
MOLREP	phasing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-12-17
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.