6YB7 | pdb_00006yb7

SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19).

• PDB DOI: https://doi.org/10.2210/pdb6YB7/pdb

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


• Deposited: 2020-03-16 Released: 2020-03-25 
• Deposition Author(s): Owen, C.D., Lukacik, P., Strain-Damerell, C.M., Douangamath, A., Powell, A.J., Fearon, D., Brandao-Neto, J., Crawshaw, A.D., Aragao, D., Williams, M., Flaig, R., Hall, D.R., McAuley, K.E., Mazzorana, M., Stuart, D.I., von Delft, F., Walsh, M.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.180 (Depositor), 0.134 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.142 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.

Douangamath, A., Fearon, D., Gehrtz, P., Krojer, T., Lukacik, P., Owen, C.D., Resnick, E., Strain-Damerell, C., Aimon, A., Abranyi-Balogh, P., Brandao-Neto, J., Carbery, A., Davison, G., Dias, A., Downes, T.D., Dunnett, L., Fairhead, M., Firth, J.D., Jones, S.P., Keeley, A., Keseru, G.M., Klein, H.F., Martin, M.P., Noble, M.E.M., O'Brien, P., Powell, A., Reddi, R.N., Skyner, R., Snee, M., Waring, M.J., Wild, C., London, N., von Delft, F., Walsh, M.A.

(2020) Nat Commun 11: 5047-5047

• PubMed: 33028810 
• DOI: https://doi.org/10.1038/s41467-020-18709-w
• Primary Citation Related Structures: 
  5R7Y, 5R7Z, 5R80, 5R81, 5R82, 5R83, 5R84, 5RE4, 5RE5, 5RE6, 5RE7, 5RE8, 5RE9, 5REA, 5REB, 5REC, 5RED, 5REE, 5REF, 5REG, 5REH, 5REI, 5REJ, 5REK, 5REL, 5REM, 5REN, 5REO, 5REP, 5RER, 5RES, 5RET, 5REU, 5REV, 5REW, 5REX, 5REY, 5REZ, 5RF0, 5RF1, 5RF2, 5RF3, 5RF4, 5RF5, 5RF6, 5RF7, 5RF8, 5RF9, 5RFA, 5RFB, ... Search all related entries


• PubMed Abstract: 
  

  COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.

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Organizational Affiliation: 
• Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.
Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel.
Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK.
Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary.
Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK.
Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK.
Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel. [e-mail].
Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK. [e-mail].
Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK. [e-mail].
Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK. [e-mail].
Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa. [e-mail].
Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK. [e-mail].
Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 34.35 kDa 
• Atom Count: 2,962 
• Modeled Residue Count: 305 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	305	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.180 (Depositor), 0.134 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.142 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.429	α = 90
b = 52.798	β = 103.03
c = 44.611	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
DIALS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-25 
Deposition Author(s): Owen, C.D., Lukacik, P., Strain-Damerell, C.M., Douangamath, A., Powell, A.J., Fearon, D., Brandao-Neto, J., Crawshaw, A.D., Aragao, D., Williams, M., Flaig, R., Hall, D.R., McAuley, K.E., Mazzorana, M., Stuart, D.I., von Delft, F., Walsh, M.A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2020-03-25
  Type: Initial release
  
• Version 2.0: 2020-04-01
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2020-04-08
  Changes: Source and taxonomy
• Version 2.2: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 2.3: 2020-10-21
  Changes: Advisory, Structure summary
• Version 3.0: 2021-12-22
  Type: Coordinate replacement
  Reason: Chirality error
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 3.1: 2023-03-29
  Changes: Structure summary
• Version 3.2: 2024-02-07
  Changes: Data collection, Refinement description
• Version 3.3: 2025-08-06
  Changes: Database references, Structure summary