Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies.
Journal, issue, pages	J. Med. Chem., Vol. 67, Page 11937-11956, Year 2024
Publish date	Feb 26, 2024 (structure data deposition date)
Authors	Dampalla, C.S. / Kim, Y. / Zabiegala, A. / Howard, D.J. / Nguyen, H.N. / Madden, T.K. / Thurman, H.A. / Cooper, A. / Liu, L. / Battaile, K.P. ...Dampalla, C.S. / Kim, Y. / Zabiegala, A. / Howard, D.J. / Nguyen, H.N. / Madden, T.K. / Thurman, H.A. / Cooper, A. / Liu, L. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C.
External links	J. Med. Chem. / PubMed:38953866
Methods	X-ray diffraction
Resolution	1.35 - 2.5 Å
Structure data	PDB-9asv: Crystal structure of SARS-CoV-2 3CL protease in complex with a benzyl 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-9asw: Crystal structure of SARS-CoV-2 3CL protease in complex with a m-fluorobenzyl 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.75 Å PDB-9asy: Crystal structure of SARS-CoV-2 3CL protease in complex with a m-chlorobenzyl 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-9asz: Crystal structure of SARS-CoV-2 3CL protease in complex with a phenylethyl 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.95 Å PDB-9at0: Crystal structure of SARS-CoV-2 3CL protease in complex with a methylcyclohexyl 2-pyrrolidone inhibitor (S-enantiomer) Method: X-RAY DIFFRACTION / Resolution: 1.85 Å PDB-9at1: Crystal structure of SARS-CoV-2 3CL protease in complex with a methylcyclohexyl 2-pyrrolidone inhibitor (R-enantiomer) Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-9at3: Crystal structure of SARS-CoV-2 3CL protease in complex with an ethylcyclohexyl 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.7 Å PDB-9at4: Crystal structure of SARS-CoV-2 3CL protease in complex with a methylbicyclo[2.2.1]heptane 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.35 Å PDB-9at5: Crystal structure of SARS-CoV-2 3CL protease in complex with a 1-methyl-4,4-difluorocyclohexyl 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.45 Å PDB-9at6: Crystal structure of SARS-CoV-2 3CL protease in complex with a methylbicyclo[2.2.1]heptene 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.4 Å PDB-9at7: Crystal structure of SARS-CoV-2 3CL protease in complex with a 2,2-difluoro-5-methylbenzo[1,3]dioxole 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.7 Å PDB-9ata: Crystal structure of MERS 3CL protease in complex with a phenylethyl 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.65 Å PDB-9atd: Crystal structure of MERS 3CL protease in complex with a ethylcyclohexyl 2-pyrrolidone inhibitor (S-enantiomer) inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-9ate: Crystal structure of MERS 3CL protease in complex with a methylbicyclo[2.2.1]heptane 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.85 Å PDB-9atf: Crystal structure of MERS 3CL protease in complex with a 1-methyl-4,4-difluorocyclohexyl 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.5 Å PDB-9atg: Crystal structure of MERS 3CL protease in complex with a 2,2-difluoro-5-methylbenzo[1,3]dioxole 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.75 Å PDB-9ath: Crystal structure of MERS 3CL protease in complex with a methylbicyclo[2.2.1]heptene 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.65 Å PDB-9ati: Crystal structure of MERS 3CL protease in complex with a racemic bicyclo[2.2.1]heptenyl-methyl 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.6 Å PDB-9atj: Crystal structure of MERS 3CL protease in complex with a m-chlorobenzyl 2-pyrrolidone inhibitor Method: X-RAY DIFFRACTION / Resolution: 1.4 Å PDB-9ats: Crystal structure of MERS 3CL protease in complex with a methylcyclohexyl 2-pyrrolidone inhibitor (S-enantiomer) Method: X-RAY DIFFRACTION / Resolution: 2.5 Å PDB-9att: Crystal structure of MERS 3CL protease in complex with a methylcyclohexyl 2-pyrrolidone inhibitor (R-enantiomer) Method: X-RAY DIFFRACTION / Resolution: 1.7 Å
Chemicals	PDB-1age: ANTAGONIST HIV-1 GAG PEPTIDES INDUCE STRUCTURAL CHANGES IN HLA B8-HIV-1 GAG PEPTIDE (GGKKKYRL-7R MUTATION) PDB-1agf: ANTAGONIST HIV-1 GAG PEPTIDES INDUCE STRUCTURAL CHANGES IN HLA B8-HIV-1 GAG PEPTIDE (GGKKRYKL-5R MUTATION) ChemComp-PG4: TETRAETHYLENE GLYCOL / precipitantYM ChemComp-HOH: WATER PDB-1agb: ANTAGONIST HIV-1 GAG PEPTIDES INDUCE STRUCTURAL CHANGES IN HLA B8-HIV-1 GAG PEPTIDE (GGRKKYKL-3R MUTATION) PDB-1aga: THE AGAROSE DOUBLE HELIX AND ITS FUNCTION IN AGAROSE GEL STRUCTURE PDB-1agi: CRYSTAL STRUCTURE OF BOVINE ANGIOGENIN AT 1.5 ANGSTROMS RESOLUTION PDB-1agj: EPIDERMOLYTIC TOXIN A FROM STAPHYLOCOCCUS AUREUS ChemComp-PO4: PHOSPHATE ION PDB-1agg: THE SOLUTION STRUCTURE OF OMEGA-AGA-IVB, A P-TYPE CALCIUM CHANNEL ANTAGONIST FROM THE VENOM OF AGELENOPSIS APERTA PDB-1agx: REFINED CRYSTAL STRUCTURE OF ACINETOBACTER GLUTAMINASIFICANS GLUTAMINASE-ASPARAGINASE PDB-1agw: CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF FIBROBLAST GROWTH FACTOR RECEPTOR 1 IN COMPLEX WITH SU4984 INHIBITOR ChemComp-MLT: D-MALATE PDB-1agz: THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE THIRD POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE PDB-1agk: THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE PDB-1agl: STRUCTURE OF A DNA-BISDAUNOMYCIN COMPLEX ChemComp-CA: Unknown entry PDB-1agn: X-RAY STRUCTURE OF HUMAN SIGMA ALCOHOL DEHYDROGENASE PDB-1agm: Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. x100 to 2.4 angstroms resolution PDB-1ago: THE SOLUTION NMR STRUCTURE OF AN (S)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE THIRD POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE PDB-1agp: THREE-DIMENSIONAL STRUCTURES AND PROPERTIES OF A TRANSFORMING AND A NONTRANSFORMING GLY-12 MUTANT OF P21-H-RAS PDB-1agq: GLIAL CELL-DERIVED NEUROTROPHIC FACTOR FROM RAT PDB-1agr: COMPLEX OF ALF4-ACTIVATED GI-ALPHA-1 WITH RGS4 PDB-1ags: A SURFACE MUTANT (G82R) OF A HUMAN ALPHA-GLUTATHIONE S-TRANSFERASE SHOWS DECREASED THERMAL STABILITY AND A NEW MODE OF MOLECULAR ASSOCIATION IN THE CRYSTAL PDB-1agt: SOLUTION STRUCTURE OF THE POTASSIUM CHANNEL INHIBITOR AGITOXIN 2: CALIPER FOR PROBING CHANNEL GEOMETRY PDB-1agh: THE SOLUTION STRUCTURE OF AN 11 BASE-PAIR OLIGONUCLEOTIDE DUPLEX CODING FOR AMINO ACIDS 60-62 OF THE PRODUCT OF THE N-RAS PROTOONCOGENE, NMR, MINIMIZED AVERAGE STRUCTURE PDB-1agv: Unknown entry PDB-1agu: THE SOLUTION NMR STRUCTURE OF THE C10R ADDUCT OF BENZO[A]PYRENE-DIOL-EPOXIDE AT THE N6 POSITION OF ADENINE OF AN 11 BASE-PAIR OLIGONUCLEOTIDE SEQUENCE CODING FOR AMINO ACIDS 60-62 OF THE PRODUCT OF THE N-RAS PROTOONCOGENE, MINIMIZED AVERAGE STRUCTURE ChemComp-MG: Unknown entry PDB-1agy*: The 1.15 angstrom refined structure of fusarium solani pisi cutinase
Source	severe acute respiratory syndrome coronavirus 2 middle east respiratory syndrome-related coronavirus
Keywords	HYDROLASE/INHIBITOR / protease / Severe Acute Respiratory Syndrome Coronavirus 2 / SARS-COV-2 3CL protease inhibitors / Covid-19 / viral protein / HYDROLASE-INHIBITOR complex / MERS / 3CL protease inhibitors