4OVZ

X-Ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4ovza2	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Papain-like viral protease catalytic domain	automated matches	(SARS coronavirus Urbani ) [TaxId: 228330 ],	SCOPe (2.08)
A	d4ovza1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	(SARS coronavirus Urbani ) [TaxId: 228330 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ubiquitin-like	8091719	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8091717	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8091717	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLpro Zn-binding domain-like	8091718	3002538	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8091717	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cysteine proteinases	8091717	3001808	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLpro Zn-binding domain-like	8091718	3002538	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Viral_protease_N	e4ovzA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Viral_protease_N	ECOD (1.6)
A	Viral_protease_C	e4ovzA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)
B	Viral_protease_C	e4ovzB1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Viral_protease_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.540	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Papain-like viral protease, N-terminal domain	CATH (4.3.0)
A	1.10.8.1190	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	2.60.120.1680	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	1.10.8.1190	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	2.60.120.1680	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Papain-like proteinase	peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds identical protein binding protein binding binding peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds identical protein binding protein binding binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups ubiquitin-like protein peptidase activity K48-linked deubiquitinase activity deubiquitinase activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding K63-linked deubiquitinase activity cysteine-type deubiquitinase activity G-quadruplex RNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms response to stimulus symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms response to stimulus symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated perturbation of host defense response response to host defenses response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses response to defenses of other organism response to external stimulus biological process involved in interaction with host symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway methylation metabolic process cellular process symbiont-mediated suppression of host ISG15-protein conjugation viral gene expression viral protein processing viral process symbiont-mediated degradation of host mRNA modulation by virus of host process virus-mediated perturbation of host defense response modulation by virus of host cellular process symbiont-mediated perturbation of host ubiquitin-like protein modification catabolic process regulation of cellular process autophagy positive regulation of biological process regulation of autophagy positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy regulation of biological process modulation by virus of host autophagy biological regulation regulation of catabolic process positive regulation of catabolic process regulation of metabolic process symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway viral genome replication viral life cycle viral translational frameshifting viral translation proteolysis primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell cytoplasm host cell part host cell endoplasmic reticulum host intracellular region host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell membrane cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell cytoplasm host cell part host cell endoplasmic reticulum host intracellular region host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasmic vesicle viral factory double membrane vesicle viral factory outer membrane double membrane vesicle viral factory host cell perinuclear region of cytoplasm host cell Golgi apparatus host cell endosome
B	Papain-like proteinase	peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds identical protein binding protein binding binding peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds identical protein binding protein binding binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups ubiquitin-like protein peptidase activity K48-linked deubiquitinase activity deubiquitinase activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding K63-linked deubiquitinase activity cysteine-type deubiquitinase activity G-quadruplex RNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms response to stimulus symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms response to stimulus symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated perturbation of host defense response response to host defenses response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host defenses response to defenses of other organism response to external stimulus biological process involved in interaction with host symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway methylation metabolic process cellular process symbiont-mediated suppression of host ISG15-protein conjugation viral gene expression viral protein processing viral process symbiont-mediated degradation of host mRNA modulation by virus of host process virus-mediated perturbation of host defense response modulation by virus of host cellular process symbiont-mediated perturbation of host ubiquitin-like protein modification catabolic process regulation of cellular process autophagy positive regulation of biological process regulation of autophagy positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy regulation of biological process modulation by virus of host autophagy biological regulation regulation of catabolic process positive regulation of catabolic process regulation of metabolic process symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway viral genome replication viral life cycle viral translational frameshifting viral translation proteolysis primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell cytoplasm host cell part host cell endoplasmic reticulum host intracellular region host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell membrane cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell cytoplasm host cell part host cell endoplasmic reticulum host intracellular region host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasmic vesicle viral factory double membrane vesicle viral factory outer membrane double membrane vesicle viral factory host cell perinuclear region of cytoplasm host cell Golgi apparatus host cell endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR022733	DPUP/SUD, C-terminal, betacoronavirus	Domain
A	IPR024358	Non-structural protein NSP3, N-terminal, betacoronavirus	Domain
A	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
A	IPR044864	Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus	Domain
A	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
A	IPR042570	Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus	Homologous Superfamily
A	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
A	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
A	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
A	IPR038166	Polyprotein cleavage domain PL2pro superfamily, betacoronavirus	Homologous Superfamily
A	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
A	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A	IPR013016	Peptidase C16, coronavirus	Domain
A	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
A	IPR044374	Non-structural protein 3, SUD-N macrodomain, SARS-CoV	Domain
A	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
A	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
A	IPR043610	Non-structural protein 6, coronavirus	Domain
A	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
A	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
A	IPR043478	Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus	Homologous Superfamily
A	IPR038400	Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus	Homologous Superfamily
A	IPR046442	NSP1, C-terminal domain, betacoronavirus	Domain
A	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
A	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A	IPR038030	NSP1 globular domain superfamily, betacoronavirus	Homologous Superfamily
A	IPR021590	NSP1, globular domain, betacoronavirus	Domain
A	IPR024375	Non-structural protein NSP3, SUD-M domain, betacoronavirus	Domain
A	IPR044367	Non-structural protein 6, betacoronavirus	Domain
A	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
A	IPR014828	Non-structural protein NSP7, coronavirus	Domain
A	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
A	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
A	IPR014829	Non-structural protein NSP8, coronavirus	Domain
A	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
A	IPR002589	Macro domain	Domain
A	IPR047567	Non-structural protein NSP3, group 2-specific marker domain, betacoronavirus	Domain
A	IPR044389	Non-structural protein 2, SARS-CoV-like	Domain
A	IPR008740	Peptidase C30, coronavirus	Domain
A	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
A	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
A	IPR049894	Coronavirus NSP3, 3Ecto domain	Domain
A	IPR043472	Macro domain-like	Homologous Superfamily
A	IPR044371	Non-structural protein 3, X-domain-like	Domain
A	IPR032592	Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus	Domain
A	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
A	IPR038083	Non-structural protein NSP3A domain-like superfamily	Homologous Superfamily
A	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B	IPR022733	DPUP/SUD, C-terminal, betacoronavirus	Domain
B	IPR024358	Non-structural protein NSP3, N-terminal, betacoronavirus	Domain
B	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
B	IPR044864	Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus	Domain
B	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
B	IPR042570	Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus	Homologous Superfamily
B	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
B	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
B	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
B	IPR038166	Polyprotein cleavage domain PL2pro superfamily, betacoronavirus	Homologous Superfamily
B	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B	IPR013016	Peptidase C16, coronavirus	Domain
B	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
B	IPR044374	Non-structural protein 3, SUD-N macrodomain, SARS-CoV	Domain
B	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
B	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
B	IPR043610	Non-structural protein 6, coronavirus	Domain
B	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
B	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
B	IPR043478	Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus	Homologous Superfamily
B	IPR038400	Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus	Homologous Superfamily
B	IPR046442	NSP1, C-terminal domain, betacoronavirus	Domain
B	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
B	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
B	IPR014822	Non-structural protein NSP9, coronavirus	Domain
B	IPR038030	NSP1 globular domain superfamily, betacoronavirus	Homologous Superfamily
B	IPR021590	NSP1, globular domain, betacoronavirus	Domain
B	IPR024375	Non-structural protein NSP3, SUD-M domain, betacoronavirus	Domain
B	IPR044367	Non-structural protein 6, betacoronavirus	Domain
B	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
B	IPR014828	Non-structural protein NSP7, coronavirus	Domain
B	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
B	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
B	IPR014829	Non-structural protein NSP8, coronavirus	Domain
B	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
B	IPR002589	Macro domain	Domain
B	IPR047567	Non-structural protein NSP3, group 2-specific marker domain, betacoronavirus	Domain
B	IPR044389	Non-structural protein 2, SARS-CoV-like	Domain
B	IPR008740	Peptidase C30, coronavirus	Domain
B	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
B	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
B	IPR049894	Coronavirus NSP3, 3Ecto domain	Domain
B	IPR043472	Macro domain-like	Homologous Superfamily
B	IPR044371	Non-structural protein 3, X-domain-like	Domain
B	IPR032592	Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus	Domain
B	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
B	IPR038083	Non-structural protein NSP3A domain-like superfamily	Homologous Superfamily
B	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210
A	OCS	Parent Component: CYS RESID: AA0205 , AA0556 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , L-cysteic acid (L-cysteine sulfonic acid) MOD:00460
B	OCS	Parent Component: CYS RESID: AA0205 , AA0556 , AA0556 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , L-cysteic acid (L-cysteine sulfonic acid) MOD:00460 , L-cysteic acid (L-cysteine sulfonic acid) MOD:00460