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Structure paper

TitleStructural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease.
Journal, issue, pagesJ. Med. Chem., Vol. 64, Page 17366-17383, Year 2021
Publish dateJun 14, 2021 (structure data deposition date)
AuthorsKneller, D.W. / Li, H. / Galanie, S. / Phillips, G. / Labbe, A. / Weiss, K.L. / Zhang, Q. / Arnould, M.A. / Clyde, A. / Ma, H. ...Kneller, D.W. / Li, H. / Galanie, S. / Phillips, G. / Labbe, A. / Weiss, K.L. / Zhang, Q. / Arnould, M.A. / Clyde, A. / Ma, H. / Ramanathan, A. / Jonsson, C.B. / Head, M.S. / Coates, L. / Louis, J.M. / Bonnesen, P.V. / Kovalevsky, A.
External linksJ. Med. Chem. / PubMed:34705466
MethodsX-ray diffraction / neutron diffraction
Resolution1.85 - 2.2 Å
Structure data

PDB-7n8c:
Joint X-ray/neutron structure of SARS-CoV-2 main protease (Mpro) in complex with Mcule5948770040
Method: X-RAY DIFFRACTION / NEUTRON DIFFRACTION / Resolution: 2.2 Å

PDB-7rls:
Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-68
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-7rm2:
Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with Mcule-CSR-494190-S1
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-7rmb:
Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-78
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-7rme:
Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-52
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-7rmt:
Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-70
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-7rmz:
Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-63
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-7rn4:
Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-69
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-7rnh:
Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-45
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-7rnk:
Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with HL-3-71
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

Chemicals

ChemComp-YD1:
6-[4-(3,4-dichlorophenyl)piperazin-1-yl]carbonyl-1~{H}-pyrimidine-2,4-dione

ChemComp-DOD:
DEUTERATED WATER

ChemComp-5YN:
6-[4-(3,4,5-trichlorophenyl)piperazine-1-carbonyl]pyrimidine-2,4(1H,3H)-dione

ChemComp-HOH:
WATER

ChemComp-5YJ:
6-[4-(3,5-dichloro-4-methylphenyl)piperazine-1-carbonyl]pyrimidine-2,4(1H,3H)-dione

ChemComp-5Z7:
6-[4-(4-bromo-3-chlorophenyl)piperazine-1-carbonyl]pyrimidine-2,4(1H,3H)-dione

ChemComp-5Z3:
6-{4-[4-chloro-3-(trifluoromethyl)phenyl]piperazine-1-carbonyl}pyrimidine-2,4(1H,3H)-dione

ChemComp-5ZN:
2-chloro-4-[4-(2,6-dioxo-1,2,5,6-tetrahydropyrimidine-4-carbonyl)piperazin-1-yl]benzaldehyde

ChemComp-5ZJ:
6-{4-[3-chloro-4-(trifluoromethyl)phenyl]piperazine-1-carbonyl}pyrimidine-2,4(1H,3H)-dione

ChemComp-H69:
6-[4-(3,4-dichlorophenyl)piperidine-1-carbonyl]pyrimidine-2,4(1H,3H)-dione

ChemComp-5ZW:
6-[4-(4-chlorophenyl)piperazine-1-carbonyl]pyrimidine-2,4(1H,3H)-dione

ChemComp-5ZT:
6-{4-[3-chloro-4-(hydroxymethyl)phenyl]piperazine-1-carbonyl}pyrimidine-2,4(3H,5H)-dione

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsHYDROLASE / cysteine protease / inhibitor complex / protonation states / HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR complex

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