5RL4

PanDDA analysis group deposition of computational designs of SARS-CoV-2 main protease covalent inhibitors -- Crystal Structure of SARS-CoV-2 main protease in complex with LON-WEI-adc59df6-3 (Mpro-x3124)

PDB DOI: https://doi.org/10.2210/pdb5RL4/pdb
Deposition Group: G_1002163 (changed state) ExploreG_1002163

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

Deposited: 2020-08-05 Released: 2020-12-02
Deposition Author(s): Fearon, D., Owen, C.D., Douangamath, A., Lukacik, P., Powell, A.J., Strain-Damerell, C.M., Zaidman, D., Krojer, T., Gehrtz, P., Wild, C., Aimon, A., Brandao-Neto, J., Carbery, A., Dunnett, L., Gorrie-Stone, T.J., Skyner, R., London, N., Walsh, M.A., von Delft, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.205
R-Value Work: 0.179
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

PanDDA analysis group deposition of computational designs of SARS-CoV-2 main protease covalent inhibitors

Fearon, D., Owen, C.D., Douangamath, A., Lukacik, P., Powell, A.J., Strain-Damerell, C.M., Zaidman, D., Krojer, T., Gehrtz, P., Wild, C., Aimon, A., Brandao-Neto, J., Carbery, A., Dunnett, L., Gorrie-Stone, T.J., Skyner, R., London, N., Walsh, M.A., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 34.49 kDa
Atom Count: 2,713
Modelled Residue Count: 304
Deposited Residue Count: 306
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	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence AnnotationsExpand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VEV (Subject of Investigation/LOI) Query on VEV Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	N-(4-tert-butylphenyl)-N-[(1R)-2-(methylamino)-2-oxo-1-(pyridin-3-yl)ethyl]propanamide C₂₁ H₂₇ N₃ O₂ ZEONMUILSPVEHQ-LJQANCHMSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.205
R-Value Work: 0.179
R-Value Observed: 0.181
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.251	α = 90
b = 52.644	β = 102.84
c = 44.3	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-12-02

Deposition Author(s):

Strain-Damerell, C.M.

Revision History (Full details and data files)

Version 1.0: 2020-12-02
Type: Initial release
Version 1.1: 2021-07-07
Changes: Database references, Structure summary
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Structure summary

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