8AJ1

SARS-CoV-2 Mpro in Complex with RK-107

PDB DOI: https://doi.org/10.2210/pdb8AJ1/pdb

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

Deposited: 2022-07-27 Released: 2024-09-11
Deposition Author(s): El Kilani, H., Hilgenfeld, R.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.275
R-Value Work: 0.195

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

SARS-CoV-2 Mpro in Complex with RK-107

El Kilani, H., Hilgenfeld, R.

To be published.

Macromolecule Content

Total Structure Weight: 34.09 kDa
Atom Count: 2,408
Modelled Residue Count: 304
Deposited Residue Count: 304
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	304	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
A1IMU (Subject of Investigation/LOI) Query on A1IMU 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]	(2R,3S)-3-[[(2S)-3-cyclopropyl-2-[2-oxidanylidene-3-(phenylcarbamoylamino)pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide C₂₇ H₃₄ N₆ O₆ KZJFPIFYXVQIAO-UGYVGDFNSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.275
R-Value Work: 0.195
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.234	α = 90
b = 52.955	β = 102.806
c = 45.707	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Funding Organization	Location	Grant Number
European Commission	European Union	--

Revision History (Full details and data files)

Version 1.0: 2024-09-11
Type: Initial release
Version 1.1: 2024-09-18
Changes: Derived calculations
Version 1.2: 2024-11-06
Changes: Structure summary

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.