3D structures of Coronavirus SARS-CoV-2 proteins and related drugs in HOMCOS server

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Last Update:20200925, Date for updating PDB:20200930

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
    A0A663DJA2 A0A663DJA2_SARS2 38
    P0DTC3 AP3A_SARS2 275 ORF3a protein; Accessory protein 3a;Protein 3a;Protein U274;Protein X1;
    P0DTC9 NCAP_SARS2 419 NC ;Protein N ; Nucleoprotein ; Nucleocapsid protein ;
    P0DTC6 NS6_SARS2 61 ns6; ORF6 protein; Accessory protein 6;Non-structural protein 6;Protein X3;
    P0DTC7 NS7A_SARS2 121 ORF7a protein; Accessory protein 7a;Protein U122;Protein X4;
    P0DTD8 NS7B_SARS2 43 ns7b; Protein non-structural 7b; Accessory protein 7b;
    P0DTC8 NS8_SARS2 121 ns8; ORF8 protein; Non-structural protein 8;
    P0DTD2 ORF9B_SARS2 97 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 protein ;sM protein ; Envelope small membrane protein ;
    P0DTC5 VME1_SARS2 222 M protein ; Membrane protein ; E1 glycoprotein ;Matrix glycoprotein ;Membrane glycoprotein ;
    P0DTD3 Y14_SARS2 73 Uncharacterized protein 14;
    P59632 AP3A_CVHSA 274 ORF3a protein; Accessory protein 3a;Protein 3a;Protein U274;Protein X1;
    P59595 NCAP_CVHSA 422 NC ;Protein N ; Nucleoprotein ; Nucleocapsid protein ;
    P59633 NS3B_CVHSA 154 ns3b; ORF3b protein; Accessory protein 3b;Non-structural protein 3b;Protein X2;
    P59634 NS6_CVHSA 63 ns6; ORF6 protein; Accessory protein 6;Non-structural protein 6;Protein X3;
    P59635 NS7A_CVHSA 122 ORF7a protein; Accessory protein 7a;Protein U122;Protein X4;
    Q7TFA1 NS7B_CVHSA 44 ns7b; Protein non-structural 7b; Accessory protein 7b;
    Q7TFA0 NS8A_CVHSA 39 ns8a; ORF8a protein; Accessory protein 8a;Protein non-structural 8a;
    Q80H93 NS8B_CVHSA 84 ns8b; ORF8b protein; Accessory protein 8b;Non-structural protein 8b;
    P59636 ORF9B_CVHSA 98 ORF9b protein; Accessory protein 9b;ORF-9b;Protein 9b;
    P0C6X7 R1AB_CVHSA 7073 pp1ab; Replicase polyprotein 1ab; ORF1ab polyprotein;
    P0C6U8 R1A_CVHSA 4382 pp1a; Replicase polyprotein 1a; ORF1a polyprotein;
    P59594 SPIKE_CVHSA 1255 S glycoprotein ; Spike glycoprotein ; E2 ;Peplomer protein ;
    P59637 VEMP_CVHSA 76 E protein ;sM protein ; Envelope small membrane protein ;
    P59596 VME1_CVHSA 221 M protein ; Membrane protein ; E1 glycoprotein ;Matrix glycoprotein ;Membrane glycoprotein ;
    Q7TLC7 Y14_CVHSA 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

    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

    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); AZM; Azasite (TN); Azithromycin (TN) AZM; Azasite (TN); Azithromycin (TN) Antibacterial, Protein biosynthesis 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 Databases-Lab, IPR, Osaka University. It is now supported by the project "Platform for Drug Discovery, Informatics, and Structural Life Science" by MEXT, Japan.

    References

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