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

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Last Update:20200610, Date for updating PDB:20200701

Proteins in pre-release 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])

    #Nprotein 45

    AC ID length
    (amino acids)
    short name full name
    A0A663DJA2 A0A663DJA2_SARS2 38
    P0DTC3 AP3A_SARS2 275 Protein 3a; Accessory protein 3a;Protein U274;Protein X1;
    P0DTC9 NCAP_SARS2 419 NC ;Protein N ; Nucleoprotein ; Nucleocapsid protein ;
    P0DTC6 NS6_SARS2 61 ns6; Non-structural protein 6; Accessory protein 6;Protein X3;
    P0DTC7 NS7A_SARS2 121 Protein 7a; Accessory protein 7a;Protein U122;Protein X4;
    P0DTD8 NS7B_SARS2 43 ns7b; Protein non-structural 7b; Accessory protein 7b;
    P0DTC8 NS8_SARS2 121 ns8; Non-structural protein 8;
    P0DTD2 ORF9B_SARS2 97 Protein 9b; Accessory protein 9b;ORF-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 Protein 3a; Accessory protein 3a;Protein U274;Protein X1;
    P59595 NCAP_CVHSA 422 NC ;Protein N ; Nucleoprotein ; Nucleocapsid protein ;
    P59633 NS3B_CVHSA 154 ns3b; Non-structural protein 3b; Accessory protein 3b;Protein X2;
    P59634 NS6_CVHSA 63 ns6; Non-structural protein 6; Accessory protein 6;Protein X3;
    P59635 NS7A_CVHSA 122 Protein 7a; Accessory protein 7a;Protein U122;Protein X4;
    Q7TFA1 NS7B_CVHSA 44 ns7b; Protein non-structural 7b; Accessory protein 7b;
    Q7TFA0 NS8A_CVHSA 39 ns8a; Protein non-structural 8a; Accessory protein 8a;
    Q80H93 NS8B_CVHSA 84 ns8b; Non-structural protein 8b; Accessory protein 8b;
    P59636 ORF9B_CVHSA 98 Protein 9b; Accessory protein 9b;ORF-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

    #Nprotein 28

    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
    D09537_2 D09537_2
    D09537_3 D09537_3
    D11472 D11472 Remdesivir (JAN/USAN); Veklury (TN) Veklury (TN) Antiviral, RNA polymerase inhibitor
    D11472_1 D11472_1
    D11472_2 D11472_2
    D11472_3 D11472_3
    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


    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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