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Structure paper

TitleTargeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors.
Journal, issue, pagesProg. Biophys. Mol. Biol., Vol. 163, Page 171-186, Year 2021
Publish dateOct 14, 2020 (structure data deposition date)
AuthorsBrosey, C.A. / Houl, J.H. / Katsonis, P. / Balapiti-Modarage, L.P.F. / Bommagani, S. / Arvai, A. / Moiani, D. / Bacolla, A. / Link, T. / Warden, L.S. ...Brosey, C.A. / Houl, J.H. / Katsonis, P. / Balapiti-Modarage, L.P.F. / Bommagani, S. / Arvai, A. / Moiani, D. / Bacolla, A. / Link, T. / Warden, L.S. / Lichtarge, O. / Jones, D.E. / Ahmed, Z. / Tainer, J.A.
External linksProg. Biophys. Mol. Biol. / PubMed:33636189
MethodsX-ray diffraction
Resolution1.43 - 2.3 Å
Structure data

PDB-7kfp:
Structure of human PARG complexed with PARG-119
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7kg0:
Structure of human PARG complexed with PARG-131
Method: X-RAY DIFFRACTION / Resolution: 1.66 Å

PDB-7kg1:
Structure of human PARG complexed with PARG-002
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-7kg3:
Crystal structure of CoV-2 Nsp3 Macrodomain
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-7kg6:
Structure of human PARG complexed with PARG-322
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-7kg7:
Structure of human PARG complexed with PARG-292
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-7kg8:
Structure of human PARG complexed with PARG-061
Method: X-RAY DIFFRACTION / Resolution: 1.43 Å

PDB-7kxb:
Crystal structure of SARS-CoV-2 Nsp3 Macrodomain complex with PARG329
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-7lg7:
Crystal structure of CoV-2 Nsp3 Macrodomain complex with PARG345
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

Chemicals

ChemComp-WD7:
N-{[2-(1,3-dimethyl-2-oxo-6-sulfanylidene-1,2,3,6-tetrahydro-7H-purin-7-yl)ethyl]carbamoyl}methanesulfonamide

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

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-HOH:
WATER / Water

ChemComp-WDA:
5-({4-[(1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl)methyl]phenyl}methyl)pyrimidine-2,4,6(1H,3H,5H)-trione

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-WDD:
1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]amino}-3,7-dihydro-1H-purine-2,6-dione

ChemComp-CAC:
CACODYLATE ION / Cacodylic acid

ChemComp-MLI:
MALONATE ION / Malonic acid

ChemComp-MES:
2-(N-MORPHOLINO)-ETHANESULFONIC ACID / pH buffer*YM / MES (buffer)

ChemComp-WDG:
1-{2-[(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)sulfanyl]ethyl}piperidine-4-carboxylic acid

ChemComp-WDJ:
8-{[2-(1,1-dioxo-1lambda~6~,4-thiazinan-4-yl)ethyl]sulfanyl}-1,3-dimethyl-3,7-dihydro-1H-purine-2,6-dione

ChemComp-WDM:
1,3-dimethyl-8-{[2-(morpholin-4-yl)-2-oxoethyl]sulfanyl}-6-sulfanylidene-1,3,6,7-tetrahydro-2H-purin-2-one

ChemComp-XB1:
N-{3-[(1,3-dimethyl-2,6-dioxo-2,3,6,9-tetrahydro-1H-purin-8-yl)sulfanyl]propyl}-N'-[2-(morpholin-4-yl)ethyl]thiourea

ChemComp-BME:
BETA-MERCAPTOETHANOL / 2-Mercaptoethanol

ChemComp-XYJ:
3-[(1,3-dimethyl-2,6-dioxo-2,3,6,9-tetrahydro-1H-purin-8-yl)sulfanyl]-N-{[2-(morpholin-4-yl)ethyl]sulfonyl}propanamide

Source
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus 2
KeywordsHYDROLASE/HYDROLASE inhibitor / HYDROLASE / hydrolase inhibitor complex / methyl xanthine / HYDROLASE-HYDROLASE inhibitor complex / SARS-CoV-2 / macrodomain

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