6YVF

Structure of SARS-CoV-2 Main Protease bound to AZD6482.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.

Gunther, S.Reinke, P.Y.A.Fernandez-Garcia, Y.Lieske, J.Lane, T.J.Ginn, H.M.Koua, F.H.M.Ehrt, C.Ewert, W.Oberthuer, D.Yefanov, O.Meier, S.Lorenzen, K.Krichel, B.Kopicki, J.D.Gelisio, L.Brehm, W.Dunkel, I.Seychell, B.Gieseler, H.Norton-Baker, B.Escudero-Perez, B.Domaracky, M.Saouane, S.Tolstikova, A.White, T.A.Hanle, A.Groessler, M.Fleckenstein, H.Trost, F.Galchenkova, M.Gevorkov, Y.Li, C.Awel, S.Peck, A.Barthelmess, M.Schlunzen, F.Lourdu Xavier, P.Werner, N.Andaleeb, H.Ullah, N.Falke, S.Srinivasan, V.Franca, B.A.Schwinzer, M.Brognaro, H.Rogers, C.Melo, D.Zaitseva-Doyle, J.J.Knoska, J.Pena-Murillo, G.E.Mashhour, A.R.Hennicke, V.Fischer, P.Hakanpaa, J.Meyer, J.Gribbon, P.Ellinger, B.Kuzikov, M.Wolf, M.Beccari, A.R.Bourenkov, G.von Stetten, D.Pompidor, G.Bento, I.Panneerselvam, S.Karpics, I.Schneider, T.R.Garcia-Alai, M.M.Niebling, S.Gunther, C.Schmidt, C.Schubert, R.Han, H.Boger, J.Monteiro, D.C.F.Zhang, L.Sun, X.Pletzer-Zelgert, J.Wollenhaupt, J.Feiler, C.G.Weiss, M.S.Schulz, E.C.Mehrabi, P.Karnicar, K.Usenik, A.Loboda, J.Tidow, H.Chari, A.Hilgenfeld, R.Uetrecht, C.Cox, R.Zaliani, A.Beck, T.Rarey, M.Gunther, S.Turk, D.Hinrichs, W.Chapman, H.N.Pearson, A.R.Betzel, C.Meents, A.

(2021) Science 372: 642-646

  • DOI: 10.1126/science.abf7945
  • Primary Citation of Related Structures:  
    6YNQ, 6YVF, 7A1U, 7ABU, 7ADW, 7AF0, 7AGA, 7AHA, 7AK4, 7AKU, 7AMJ, 7ANS, 7AOL, 7AP6, 7APH, 7AQE, 7AQI, 7AQJ, 7AR5, 7AR6, 7ARF, 7AVD, 7AWR, 7AWS, 7AWU, 7AWW, 7AX6, 7AXM, 7AXO, 7AY7, 7B83, 7NEV

  • PubMed Abstract: 
  • The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (M pro ), which is essential for viral replication ...

    The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (M pro ), which is essential for viral replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to M pro In subsequent cell-based viral reduction assays, one peptidomimetic and six non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.


    Related Citations: 
    • Inhibition of SARS-CoV-2 main protease by allosteric drug-binding
      Guenther, S., Reinke, P.Y.A.,, Fernandez-Garcia, Y.,, Lieske, J.,, Lane, T.J.,, Ginn, H.M.,, Koua, F.H.M.,, Ehrt, C.,, Ewert, W.,, Oberthuer, D.,, Yefanov, O.,, Meier, S.,, Lorenzen, K.,, Krichel, B.,, Kopicki, J.D.,, Gelisio, L.,, Brehm, W.,, Dunkel , I.,, Seychell , B.,, Gieseler , H.,, Norton-Baker , B.,, Escudero-Perez, B.,, Domaracky , M.,, Saouane, S.,, Tolstikova , A.,, White, T.A.,, Hanle, A.,, Groessler , M.,, Fleckenstein , H.,, Trost , F.,, Galchenkova , M.,, Gevorkov , Y.,, Li , C.,, Awel , S.,, Peck, A., Barthelmess , M.,, Schluenzen , F.,, Paulraj , L.X.,, Werner , N.,, Andaleeb , H.,, Ullah , N.,, Falke , S.,, Srinivasan, V.,, Franca , B.,, Schwinzer , M.,, Brognaro , H.,, Rogers , C.,, Melo , D.,, Doyle , J.J.,, Knoska , J.,, Pena Murillo, G.E.,, Rahmani Mashhour, A.,, Guicking , F.,, Hennicke , V.,, Fischer , P.,, Hakanpaeae , J.,, Meyer , J.,, Gribbon , P.,, Ellinger , B.,, Kuzikov , M.,, Wolf , M.,, Burenkov, G.,, von Stetten, D.,, Pompidor, G.,, Bento, I.,, Panneerselvam, S.,, Karpics, I.,, Schneider , T.R.,, Garcia Alai, M.,, Niebling, S.,, Guenther , C.,, Schmidt , C.,, Schubert , R.,, Han , H.,, Boger, J.,, Monteiro , D.,, Zhang, L.,, Sun, X.,, Pletzer-Zelgert , J.,, Wollenhaupt , J.,, Feiler , C.,, Weiss , M.,, Schulz , E.C.,, Mehrabi , P.,, Karnicar , K.,, Usenik, A.,, Loboda , J.,, Tidow , H.,, Chari , A.,, Hilgenfeld , R.,, Uetrecht , C.,, Cox , R.,, Zaliani , A.,, Beck , T.,, Rarey , M.,, Guenther , S.,, Turk , D.,, Hinrichs , W.,, Chapman , H.N.,, Pearson , A.,, Betzel , C.,, Meents , A.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Center for Free-Electron Laser Science, DESY, Notkestr. 85, 22607 Hamburg, Germany. sebastian.guenther@desy.de alke.meents@desy.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A82 (Subject of Investigation/LOI)
Query on A82

Download Ideal Coordinates CCD File 
B [auth A]2-[[(1R)-1-(7-methyl-2-morpholin-4-yl-4-oxidanylidene-pyrido[1,2-a]pyrimidin-9-yl)ethyl]amino]benzoic acid
C22 H24 N4 O4
IRTDIKMSKMREGO-OAHLLOKOSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
L [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.153α = 90
b = 53.645β = 102.313
c = 44.595γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2020-12-09
    Changes: Database references
  • Version 1.3: 2021-04-14
    Changes: Author supporting evidence, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2021-05-19
    Changes: Database references