3D structures of proteins and compounds related to Coronavirus SARS-CoV-2

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Last Update:2021/06/11, Date for updating PDB:20210609

We summarize 3D structures of proteins in Coronavirus SARS-CoV-2 that causes coronavirus disease 2019 (COVID-19) in a following table.
We provide analyses "Searching Contact Molecules with Query Protein" of HOMCOS for each protein of the virus. Monomeric and bound 3D structures of the virus proteins and their homologs are summarized. Found 3D structures can be used for templates of homology modeling. Details of the usage are explained in the HELP page.
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Proteins in UniProt

Amino acid sequences of SARS-CoV-2 were taken from UniProt pre_release files. They include entries for the SARS-CoV-2 virus (proteome UP000464024) and SARS-CoV virus (proteome UP000000354) and human target proteins. ([HEAD_LINE] [FTP_SITE])

AC	ID	length (amino acids)	short name	full name
P0DTC3	AP3A_SARS2	275	ORF3a;	ORF3a protein; Accessory protein 3a;Protein 3a;Protein U274;Protein X1;
P0DTC9	NCAP_SARS2	419	N; NC ;Protein N ;	Nucleoprotein ; Nucleocapsid protein ;
P0DTC6	NS6_SARS2	61	ORF6; ns6;	ORF6 protein; Accessory protein 6;Non-structural protein 6;Protein X3;
P0DTC7	NS7A_SARS2	121	ORF7a;	ORF7a protein; Accessory protein 7a;Protein U122;Protein X4;
P0DTD8	NS7B_SARS2	43	ORF7b;	ORF7b protein; Accessory protein 7b;
P0DTC8	NS8_SARS2	121	ORF8; ns8;	ORF8 protein; Non-structural protein 8;
P0DTD2	ORF9B_SARS2	97	ORF9b;	ORF9b protein; Accessory protein 9b;ORF-9b;Protein 9b;
P0DTD1	R1AB_SARS2	7096	pp1ab;	Replicase polyprotein 1ab; ORF1ab polyprotein;
P0DTC1	R1A_SARS2	4405	pp1a;	Replicase polyprotein 1a; ORF1a polyprotein;
P0DTC2	SPIKE_SARS2	1273	S glycoprotein ;	Spike glycoprotein ; E2 ;Peplomer protein ;
P0DTC4	VEMP_SARS2	75	E;sM protein ;	Envelope small membrane protein ;
P0DTC5	VME1_SARS2	222	M;	Membrane protein ; E1 glycoprotein ;Matrix glycoprotein ;Membrane glycoprotein ;
P0DTD3	ORF9C_SARS2	73	ORF9c; ORF14;	ORF9c protein ; Uncharacterized protein 14;
P59632	AP3A_SARS	274		ORF3a protein; Accessory protein 3a;Protein 3a;Protein U274;Protein X1;
P59595	NCAP_SARS	422	NC ;Protein N ;	Nucleoprotein ; Nucleocapsid protein ;
P59633	NS3B_SARS	154	ns3b;	ORF3b protein; Accessory protein 3b;Non-structural protein 3b;Protein X2;
P59634	NS6_SARS	63	ns6;	ORF6 protein; Accessory protein 6;Non-structural protein 6;Protein X3;
P59635	NS7A_SARS	122		ORF7a protein; Accessory protein 7a;Protein U122;Protein X4;
Q7TFA1	NS7B_SARS	44	ns7b;	Protein non-structural 7b; Accessory protein 7b;
Q7TFA0	NS8A_SARS	39	ns8a;	ORF8a protein; Accessory protein 8a;Protein non-structural 8a;
Q80H93	NS8B_SARS	84	ns8b;	ORF8b protein; Accessory protein 8b;Non-structural protein 8b;
P59636	ORF9B_SARS	98		ORF9b protein; Accessory protein 9b;ORF-9b;Protein 9b;
P0C6X7	R1AB_SARS	7073	pp1ab;	Replicase polyprotein 1ab; ORF1ab polyprotein;
P0C6U8	R1A_SARS	4382	pp1a;	Replicase polyprotein 1a; ORF1a polyprotein;
P59594	SPIKE_SARS	1255	S glycoprotein ;	Spike glycoprotein ; E2 ;Peplomer protein ;
P59637	VEMP_SARS	76	E protein ;sM protein ;	Envelope small membrane protein ;
P59596	VME1_SARS	221	M protein ;	Membrane protein ; E1 glycoprotein ;Matrix glycoprotein ;Membrane glycoprotein ;
Q7TLC7	Y14_SARS	70		Uncharacterized protein 14;
Q9BYF1	ACE2_HUMAN	805	ACEH ;ACE-related carboxypeptidase;	Angiotensin-converting enzyme 2; Angiotensin-converting enzyme homolog ;Angiotensin-converting enzyme-related carboxypeptidase ;Metalloprotease MPROT15 {ECO:0000303\|Ref.6};
Q10589	BST2_HUMAN	180	BST-2;	Bone marrow stromal antigen 2; HM1.24 antigen;Tetherin;
Q92499	DDX1_HUMAN	740	DBP-RB;	ATP-dependent RNA helicase DDX1; DEAD box protein 1;DEAD box protein retinoblastoma;
P09958	FURIN_HUMAN	794	PACE;	Furin; Dibasic-processing enzyme;Paired basic amino acid residue-cleaving enzyme;
P52292	IMA1_HUMAN	529		Importin subunit alpha-1 ; Karyopherin subunit alpha-2;RAG cohort protein 1;SRP1-alpha;
P20701	ITAL_HUMAN	1170	LFA-1A;	Integrin alpha-L; CD11 antigen-like family member A;Leukocyte adhesion glycoprotein LFA-1 alpha chain;Leukocyte function-associated molecule 1 alpha chain;
Q8N3R9	MPP5_HUMAN	675		MAGUK p55 subfamily member 5;
Q99623	PHB2_HUMAN	299		Prohibitin-2; B-cell receptor-associated protein BAP37;D-prohibitin;Repressor of estrogen receptor activity;
P35232	PHB_HUMAN	272		Prohibitin ;
O43765	SGTA_HUMAN	313	UBP;	Small glutamine-rich tetratricopeptide repeat-containing protein alpha; Alpha-SGT;Vpu-binding protein;
P84022	SMAD3_HUMAN	425	MAD homolog 3;Mad3;Mothers against DPP homolog 3;hMAD-3; SMAD 3;Smad3;hSMAD3;	Mothers against decapentaplegic homolog 3; JV15-2;SMAD family member 3;
O15393	TMPS2_HUMAN	492		Transmembrane protease serine 2 ; Serine protease 10 ;
P15144	AMPN_HUMAN	967	AP-N;hAPN; AP-M;	Aminopeptidase N ; Alanyl aminopeptidase;Aminopeptidase M;Microsomal aminopeptidase;Myeloid plasma membrane glycoprotein CD13;gp150;
P08887	IL6RA_HUMAN	468	IL-6 receptor subunit alpha;IL-6R subunit alpha;IL-6R-alpha;IL-6RA; gp80;	Interleukin-6 receptor subunit alpha ; IL-6R 1;Membrane glycoprotein 80;
P40189	IL6RB_HUMAN	918	IL-6 receptor subunit beta;IL-6R subunit beta;IL-6R-beta;IL-6RB; gp130 ;	Interleukin-6 receptor subunit beta ; CDw130;Interleukin-6 signal transducer;Membrane glycoprotein 130;Oncostatin-M receptor subunit alpha;
P05231	IL6_HUMAN	212	IL-6; BSF-2;CDF;IFN-beta-2;	Interleukin-6 ; B-cell stimulatory factor 2;CTL differentiation factor;Hybridoma growth factor;Interferon beta-2;

Proteins in Genpept

Amino acid sequences of SARS-CoV-2 were taken from NCBI Reference Sequence. ([NC_045512]Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome)

protein_id	length (amino acids)	product	gene	note
YP_009724389.1	7096	2'-O-ribose methyltransferase	orf1ab	pp1ab; translated by -1 ribosomal frameshift
YP_009725297.1	180	leader protein		nsp1; produced by both pp1a and pp1ab
YP_009725298.1	638	nsp2		produced by both pp1a and pp1ab
YP_009725299.1	1945	nsp3		former nsp1; conserved domains are: N-terminal
YP_009725300.1	500	nsp4		nsp4B_TM; contains transmembrane domain 2 (TM2);
YP_009725301.1	306	3C-like proteinase		nsp5A_3CLpro and nsp5B_3CLpro; main proteinase
YP_009725302.1	290	nsp6		nsp6_TM; putative transmembrane domain; produced by
YP_009725303.1	83	nsp7		produced by both pp1a and pp1ab
YP_009725304.1	198	nsp8		produced by both pp1a and pp1ab
YP_009725305.1	113	nsp9		ssRNA-binding protein; produced by both pp1a and
YP_009725306.1	139	nsp10		nsp10_CysHis; formerly known as growth-factor-like
YP_009725307.1	932	RNA-dependent RNA polymerase		nsp12; NiRAN and RdRp; produced by pp1ab only
YP_009725308.1	601	helicase		nsp13_ZBD, nsp13_TB, and nsp_HEL1core; zinc-binding
YP_009725309.1	527	3'-to-5' exonuclease		nsp14A2_ExoN and nsp14B_NMT; produced by pp1ab
YP_009725310.1	346	endoRNAse		nsp15-A1 and nsp15B-NendoU; produced by pp1ab only
YP_009725311.1	298	2'-O-ribose methyltransferase		nsp16_OMT; 2'-o-MT; produced by pp1ab only
YP_009725295.1	4405	nsp11	orf1ab	pp1a
YP_009725312.1	13	nsp11		produced by pp1a only
YP_009724390.1	1273	surface glycoprotein	S	structural protein; spike protein
YP_009724391.1	275	ORF3a protein	ORF3a
YP_009724392.1	75	envelope protein	E	ORF4; structural protein; E protein
YP_009724393.1	222	membrane glycoprotein	M	ORF5; structural protein
YP_009724394.1	61	ORF6 protein	ORF6
YP_009724395.1	121	ORF7a protein	ORF7a
YP_009725318.1	43	ORF7b	ORF7b
YP_009724396.1	121	ORF8 protein	ORF8
YP_009724397.2	419	nucleocapsid phosphoprotein	N	ORF9; structural protein
YP_009725255.1	38	ORF10 protein	ORF10

Reported Efficient Drugs

3D bound protein structures with compounds reported in COVID-19 drug development and COVID-19 drug repurposing research are summarized in a following table.
We provide analyses "Searching Contact Proteins with Query Compound" of HOMCOS for each compound. Bound protein 3D structures with the compound and its analogues are summarized.

KEGG_ID	structure	NAME	OTHER NAME	EFFICACY
D01703		D01703 Ciclesonide (JAN/USAN/INN); Alvesco (TN); Omnaris (TN); Zetonna (TN)	Alvesco (TN); Omnaris (TN); Zetonna (TN)	Antiasthmatic, Anti-inflammatory, Glucocorticoid receptor agonist
D01425		D01425 Lopinavir (JAN/USP/INN)		Antiviral, HIV protease inhibitor
D00427		D00427 Ritonavir (JAN/USP/INN); Norvir (TN)	Norvir (TN)	Antiviral, HIV protease inhibitor
D09537		D09537 Favipiravir (JAN/USAN/INN); Avigan (TN)	Avigan (TN)	Antiviral, RNA replicase inhibitor
D09537_1		D09537_1 Favipiravir-MTP; Active form of Favipiravir;	Active form of Favipiravir;	Antiviral, RNA replicase inhibitor
D09537_2		D09537_2 Favipiravir-DTP; Active form of Favipiravir;	Active form of Favipiravir;	Antiviral, RNA replicase inhibitor
D09537_3		D09537_3 Favipiravir-RTP; Active form of Favipiravir;	Active form of Favipiravir;	Antiviral, RNA replicase inhibitor
D11472		D11472 Remdesivir (JAN/USAN); Veklury (TN)	Veklury (TN)	Antiviral, RNA polymerase inhibitor
D11472_1		D11472_1 Remdesivir-monophosphate (USAN		Antiviral
D11472_2		D11472_2 Remdesivir-diphosphate (USAN		Antiviral
D11472_3		D11472_3 Remdesivir-triphosphate (USAN		Antiviral
D02366		D02366 Chloroquine (USP/INN)		Antimalarial, Amebicide
D08050		D08050 Hydroxychloroquine (INN); Polirreumin (TN)	Polirreumin (TN)	Antimalarial
D01670		D01670 Nafamostat mesylate (USAN); Nafamostat mesilate (JP17); Ronastat (TN)	Nafamostat mesilate (JP17); Ronastat (TN)	Anticoagulant, Antifibrinolytic, Serine protease inhibitor
D00429		D00429 Saquinavir (JAN/USP/INN); Fortovase (TN)	Fortovase (TN)	Antiviral, HIV protease inhibitor
D01035		D01035 Cepharanthine (JAN); Cepharanthine (TN)	Cepharanthine (TN)	Antiallergic, Blood circulation promotor
D00804		D00804 Ivermectin (JAN/USP/INN); Sklice (TN); Soolantra (TN); Stromectol (TN)	Sklice (TN); Soolantra (TN); Stromectol (TN)	Antiparasitic
D00292		D00292 Dexamethasone (JP17/USP/INN); Decadron (TN); Maxidex (TN)	Decadron (TN); Maxidex (TN)	Anti-inflammatory, Antipruritic, Glucocorticoid receptor agonist
D07486		D07486 Azithromycin (INN); Azasite (TN); Azithromycin (TN)	Azasite (TN); Azithromycin (TN)	Antibacterial, Protein biosynthesis inhibitor
D08897		D08897 Dapagliflozin (USAN/INN); Forxiga (TN)	Forxiga (TN)	Antidiabetic, SGLT-2 inhibitor
D00570		D00570 Colchicine (JP17/USP); Colchicine (TN)	Colchicine (TN)	Gout suppressant, Leukocyte (neutrophil) migration inhibitor, Tubulin polymerization inhibitor
D07606		D07606 Camostat (INN)		Anti-inflammatory, Serine protease inhibitor
D10308		D10308 Baricitinib (JAN/USAN/INN); Olumiant (TN)	Olumiant (TN)	Anti-inflammatory, Antirheumatic, Immunosuppressant, Janus kinase (JAK) inhibitor

BLAST is employed for the amino acids sequence search, KCOMBU is used for the chemical structure search.

HOMCOS is developed and maintained by Protein Data Bank Japan, IPR, Osaka University. It is now supported by the project "Platform for Drug Discovery, Informatics, and Structural Life Science" by MEXT, Japan.

References

Kawabata T. (2016) HOMCOS: an update server to search and model complex 3D structures. J.Struct.Funct.Genomics. 17,83-99. [PubMed] [Publisher]
Fukuhara N., Kawabata T. (2008) HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures. Nucleic Acids Res., 36, W185-W189. [PubMed]

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