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Structure paper

TitleX-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.
Journal, issue, pagesScience, Vol. 372, Page 642-646, Year 2021
Publish dateApr 14, 2020 (structure data deposition date)
AuthorsGunther, 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. ...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. / Turk, D. / Hinrichs, W. / Chapman, H.N. / Pearson, A.R. / Betzel, C. / Meents, A.
External linksScience / PubMed:33811162
MethodsX-ray diffraction
Resolution1.34 - 2.59 Å
Structure data

PDB-6ynq:
Structure of SARS-CoV-2 Main Protease bound to 2-Methyl-1-tetralone.
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-6yvf:
Structure of SARS-CoV-2 Main Protease bound to AZD6482.
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7a1u:
Structure of SARS-CoV-2 Main Protease bound to Fusidic Acid.
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-7abu:
Structure of SARS-CoV-2 Main Protease bound to RS102895
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-7adw:
Structure of SARS-CoV-2 Main Protease bound to 2,4'-Dimethylpropiophenone.
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-7af0:
Structure of SARS-CoV-2 Main Protease bound to Ipidacrine.
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7aga:
Structure of SARS-CoV-2 Main Protease bound to AT7519
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

PDB-7aha:
Structure of SARS-CoV-2 Main Protease bound to Maleate.
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

PDB-7ak4:
Structure of SARS-CoV-2 Main Protease bound to Tretazicar.
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-7aku:
Structure of SARS-CoV-2 Main Protease bound to Calpeptin.
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-7amj:
Structure of SARS-CoV-2 Main Protease bound to PD 168568.
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-7ans:
Structure of SARS-CoV-2 Main Protease bound to Adrafinil.
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7aol:
Structure of SARS-CoV-2 Main Protease bound to Climbazole
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-7ap6:
Structure of SARS-CoV-2 Main Protease bound to MUT056399.
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-7aph:
Structure of SARS-CoV-2 Main Protease bound to Tofogliflozin.
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7aqe:
Structure of SARS-CoV-2 Main Protease bound to UNC-2327
Method: X-RAY DIFFRACTION / Resolution: 1.39 Å

PDB-7aqi:
Structure of SARS-CoV-2 Main Protease bound to Ifenprodil
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7aqj:
Structure of SARS-CoV-2 Main Protease bound to Triglycidyl isocyanurate.
Method: X-RAY DIFFRACTION / Resolution: 2.59 Å

PDB-7ar5:
Structure of apo SARS-CoV-2 Main Protease with small beta angle, space group C2.
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7ar6:
Structure of apo SARS-CoV-2 Main Protease with large beta angle, space group C2.
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7arf:
Structure of SARS-CoV-2 Main Protease bound to thioglucose.
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-7avd:
Structure of SARS-CoV-2 Main Protease bound to SEN1269 ligand
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7awr:
Structure of SARS-CoV-2 Main Protease bound to Tegafur
Method: X-RAY DIFFRACTION / Resolution: 1.34 Å

PDB-7aws:
Structure of SARS-CoV-2 Main Protease bound to TH-302.
Method: X-RAY DIFFRACTION / Resolution: 1.81 Å

PDB-7awu:
Structure of SARS-CoV-2 Main Protease bound to LSN2463359.
Method: X-RAY DIFFRACTION / Resolution: 2.07 Å

PDB-7aww:
Structure of SARS-CoV-2 Main Protease bound to Clonidine
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7ax6:
Structure of SARS-CoV-2 Main Protease bound to Glutathione isopropyl ester
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-7axm:
Structure of SARS-CoV-2 Main Protease bound to Pelitinib
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7axo:
Structure of SARS-CoV-2 Main Protease bound to AR-42.
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7ay7:
Structure of SARS-CoV-2 Main Protease bound to Isofloxythepin
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-7b83:
Structure of SARS-CoV-2 Main Protease bound to pyrithione zinc
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7nev:
Structure of the hemiacetal complex between the SARS-CoV-2 Main Protease and Leupeptin
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

Chemicals

ChemComp-P6N:
(2~{S})-2-methyl-3,4-dihydro-2~{H}-naphthalen-1-one

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM / Dimethyl sulfoxide

ChemComp-CL:
Unknown entry / Chloride

ChemComp-HOH:
WATER / Water

ChemComp-A82:
2-[[(1R)-1-(7-methyl-2-morpholin-4-yl-4-oxidanylidene-pyrido[1,2-a]pyrimidin-9-yl)ethyl]amino]benzoic acid

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

ChemComp-CA:
Unknown entry

ChemComp-FUA:
FUSIDIC ACID / antibiotic, Antimicrobial*YM / Fusidic acid

ChemComp-IMD:
IMIDAZOLE / Imidazole

ChemComp-R6Q:
1'-[2-[4-(trifluoromethyl)phenyl]ethyl]spiro[1~{H}-3,1-benzoxazine-4,4'-piperidine]-2-one

ChemComp-R7Q:
2-methyl-1-(4-methylphenyl)propan-1-one

ChemComp-R9W:
2,3,5,6,7,8-hexahydro-1~{H}-cyclopenta[b]quinolin-9-amine / inhibitor*YM / Ipidacrine

ChemComp-LZE:
4-{[(2,6-dichlorophenyl)carbonyl]amino}-N-piperidin-4-yl-1H-pyrazole-3-carboxamide

ChemComp-SIN:
SUCCINIC ACID / Succinic acid

ChemComp-CB1:
5-(AZIRIDIN-1-YL)-2,4-DINITROBENZAMIDE

ChemComp-RMZ:
(3~{S})-3-[2-[4-(3,4-dimethylphenyl)piperazin-1-yl]ethyl]-2,3-dihydroisoindol-1-one

ChemComp-RNW:
2-[(diphenylmethyl)-oxidanyl-$l^{3}-sulfanyl]-~{N}-oxidanyl-ethanamide

ChemComp-RQH:
(1~{S})-1-(4-chloranylphenoxy)-1-imidazol-1-yl-3,3-dimethyl-butan-2-one / antifungal*YM / Climbazole

ChemComp-RQN:
4-(4-ethyl-5-fluoranyl-2-oxidanyl-phenoxy)-3-fluoranyl-benzamide

ChemComp-RT2:
Tofogliflozin / inhibitor*YM / Tofogliflozin

ChemComp-RV5:
N-1,2,3-Benzothiadiazol-6-yl-N'-[2-oxo-2-(1-piperidinyl)ethyl]urea also called unc-2327

ChemComp-QEL:
4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol / inhibitor*YM / Ifenprodil

ChemComp-S7H:
1-[(2~{R})-2-oxidanylpropyl]-3-[[(2~{R})-oxiran-2-yl]methyl]-5-[[(2~{S})-oxiran-2-yl]methyl]-1,3,5-triazinane-2,4,6-trione

ChemComp-RV8:
Triglycidyl isocyanurate

ChemComp-RVW:
(2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-sulfanyl-oxane-3,4,5-triol

ChemComp-S1W:
3-[[5-[3-(dimethylamino)phenoxy]pyrimidin-2-yl]amino]phenol

ChemComp-S7W:
TEGAFUR / Tegafur

ChemComp-S8E:
5-[[(2-bromoethylamino)-(ethylamino)phosphoryl]oxymethyl]-1-methyl-~{N},~{N}-bis(oxidanyl)imidazol-2-amine

ChemComp-S8B:
~{N}-propan-2-yl-5-(2-pyridin-4-ylethynyl)pyridine-2-carboxamide

ChemComp-CLU:
2,6-DICHLORO-N-IMIDAZOLIDIN-2-YLIDENEANILINE / medication, agonist*YM / Clonidine

ChemComp-S8H:
(2~{S})-2-azanyl-5-oxidanylidene-5-[[(2~{S})-1-oxidanylidene-1-[(2-oxidanylidene-2-propan-2-yloxy-ethyl)amino]-3-sulfanyl-propan-2-yl]amino]pentanoic acid

ChemComp-93J:
(2E)-N-{4-[(3-chloro-4-fluorophenyl)amino]-3-cyano-7-ethoxyquinolin-6-yl}-4-(dimethylamino)but-2-enamide

ChemComp-QCP:
AR-42 / inhibitor*YM / Histone deacetylase inhibitor

ChemComp-S8T:
9-fluoranyl-3-propan-2-yl-5,6-dihydrobenzo[b][1]benzothiepine

ChemComp-PK8:
9-oxa-7-thia-1-azonia-8$l^{2}-zincabicyclo[4.3.0]nona-1,3,5-triene

Source
  • severe acute respiratory syndrome coronavirus 2
  • synthetic construct (others)
  • streptomyces roseus (bacteria)
KeywordsPEPTIDE BINDING PROTEIN / SARS-CoV-2 / mPro / COVID-19 / COVID-!9 / HYDROLASE / virus protease / inhibitor / complex / screen / Main protease / anti-viral / Covid-19 pandemic

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