Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T87374 | Target Info | |||
| Target Name | COVID-19 spike glycoprotein (S) | ||||
| Synonyms | COVID-19 S glycoprotein; COVID-19 E2; COVID-19 Peplomer protein | ||||
| Gene Name | COVID-19 S | ||||
| Biochemical Class | Betacoronaviruses spike protein family | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Tretinoin | Ligand Info | |||||
| Structure Description | Cryo-EM structure of the SARS-CoV-2 spike glycoprotein in complex with all-trans retinoic acid | PDB:7Y42 | ||||
| Method | Electron microscopy | Resolution | 3.45 Å | Mutation | Yes | [1] |
| PDB Sequence |
AYTNSFTRGV
36 YYPDKVFRSS46 VLHSTQDLFL56 PFFSNVTWFH66 AIHVGVYFAS94 SNIIRGWIFG 107 TTLDSKTQSL117 LIVNNATNVV127 IKVCFTFEYV171 SQKNLREFVF194 FKIYSKHTPD 215 LPQGFSALEV227 DLPIGINIAY265 YVGYLQPRTF275 LLKYNENGTI285 TDAVDCALDP 295 LSETKCTLKS305 FTVEKGIYQT315 SNTESIVRFP330 NITNLCPFGE340 VFNATRFASV 350 YAWNRKRISN360 CVADYSVLYN370 SASFSTFKCY380 GVSPTKLNDL390 CFTNVYADSF 400 VIRGDEVRQI410 APGQTGKIAD420 YNYKLPDDFT430 GCVIAWNSNN440 LDSKGNYNYL 452 YRLFRKSNLK462 PFERDISTEI472 YQAGSTPCNG482 VEGFNCYFPL492 QSYGFQPTNG 502 VGYQPYRVVV512 LSFELLHAPA522 TVCGPKKSTN532 LVKNKCVNFN542 FNGLTGTGVL 552 TESNKKFLPF562 QQFGRDIADT572 TDAVRDPQTL582 EILDITPCSF592 GGVSVITPGT 602 NTSNQVAVLY612 QDVNCTEVPD627 QLTPTWRVYS637 TGSNVFQTRA647 GCLIGAEHVN 657 NSYECDIPIG667 AGICASYQTS689 QSIIAYTMSL699 GAENSVAYSN709 NSIAIPTNFT 719 ISVTTEILPV729 SMTKTSVDCT739 MYICGDSTEC749 SNLLLQYGSF759 CTQLNRALTG 769 IAVEQDKNTQ779 EVFAQVKQIY789 KTPPIKDFGG799 FNFSQILPDP809 SKPSKRSFIE 819 DLLFNKVTDL849 ICAQKFNGLT859 VLPPLLTDEM869 IAQYTSALLA879 GTITSGWTFG 889 AGAALQIPFA899 MQMAYRFNGI909 GVTQNVLYEN919 QKLIANQFNS929 AIGKIQDSLS 939 STASALGKLQ949 DVVNQNAQAL959 NTLVKQLSSN969 FGAISSVLND979 ILSRLDPPEA 989 EVQIDRLITG999 RLQSLQTYVT1009 QQLIRAAEIR1019 ASANLAATKM1029 SECVLGQSKR 1039 VDFCGKGYHL1049 MSFPQSAPHG1059 VVFLHVTYVP1069 AQEKNFTTAP1079 AICHDGKAHF 1089 PREGVFVSNG1099 THWFVTQRNF1109 YEPQIITTDN1119 TFVSGNCDVV1129 IGIVNNTVYD 1139 PLQPELDS
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| Ligand Name: Linoleic acid | Ligand Info | |||||
| Structure Description | SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C3 symmetry | PDB:7QUR | ||||
| Method | Electron microscopy | Resolution | 2.27 Å | Mutation | Yes | [2] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVSGT 73 NGTKRFDNPV83 LPFNDGVYFA93 STEKSNIIRG103 WIFGTTLDSK113 TQSLLIVNNA 123 TNVVIKVCEF133 QFCNDPFLGV143 YYHKNNKSWM153 ESEFRVYSSA163 NNCTFEYVSQ 173 PFLMDLEGKQ183 GNFKNLREFV193 FKNIDGYFKI203 YSKHTPINLV213 RDLPQGFSAL 223 EPLVDLPIGI233 NITRFQTLLA243 LHRSYLTPGD253 SSSGWTAGAA263 AYYVGYLQPR 273 TFLLKYNENG283 TITDAVDCAL293 DPLSETKCTL303 KSFTVEKGIY313 QTSNFRVQPT 323 ESIVRFPNIT333 NLCPFGEVFN343 ATRFASVYAW353 NRKRISNCVA363 DYSVLYNSAS 373 FSTFKCYGVS383 PTKLNDLCFT393 NVYADSFVIR403 GDEVRQIAPG413 QTGKIADYNY 423 KLPDDFTGCV433 IAWNSNNLDS443 KVGGNYNYLY453 RLFRKSNLKP463 FERDISTEIY 473 QAGSTPCNGV483 EGFNCYFPLQ493 SYGFQPTNGV503 GYQPYRVVVL513 SFELLHAPAT 523 VCGPKKSTNL533 VKNKCVNFNF543 NGLTGTGVLT553 ESNKKFLPFQ563 QFGRDIADTT 573 DAVRDPQTLE583 ILDITPCSFG593 GVSVITPGTN603 TSNQVAVLYQ613 DVNCTTWRVY 636 STGSNVFQTR646 AGCLIGAEHV656 NNSYECDIPI666 GAGICASYQT676 SQSIIAYTMS 698 LGAENSVAYS708 NNSIAIPTNF718 TISVTTEILP728 VSMTKTSVDC738 TMYICGDSTE 748 CSNLLLQYGS758 FCTQLNRALT768 GIAVEQDKNT778 QEVFAQVKQI788 YKTPPIKDFG 798 GFNFSQILPD808 PSKPSKRSFI818 EDLLFNKVTL828 ADAGFIKQYG838 DCLGDIAARD 848 LICAQKFNGL858 TVLPPLLTDE868 MIAQYTSALL878 AGTITSGWTF888 GAGAALQIPF 898 AMQMAYRFNG908 IGVTQNVLYE918 NQKLIANQFN928 SAIGKIQDSL938 SSTASALGKL 948 QDVVNQNAQA958 LNTLVKQLSS968 NFGAISSVLN978 DILSRLDKVE988 AEVQIDRLIT 998 GRLQSLQTYV1008 TQQLIRAAEI1018 RASANLAATK1028 MSECVLGQSK1038 RVDFCGKGYH 1048 LMSFPQSAPH1058 GVVFLHVTYV1068 PAQEKNFTTA1078 PAICHDGKAH1088 FPREGVFVSN 1098 GTHWFVTQRN1108 FYEPQIITTD1118 NTFVSGNCDV1128 VIGIVNNTVY1138 D |
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: O-Sialic Acid | Ligand Info | |||||
| Structure Description | SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C3 symmetry | PDB:7QUR | ||||
| Method | Electron microscopy | Resolution | 2.27 Å | Mutation | Yes | [2] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVSGT 73 NGTKRFDNPV83 LPFNDGVYFA93 STEKSNIIRG103 WIFGTTLDSK113 TQSLLIVNNA 123 TNVVIKVCEF133 QFCNDPFLGV143 YYHKNNKSWM153 ESEFRVYSSA163 NNCTFEYVSQ 173 PFLMDLEGKQ183 GNFKNLREFV193 FKNIDGYFKI203 YSKHTPINLV213 RDLPQGFSAL 223 EPLVDLPIGI233 NITRFQTLLA243 LHRSYLTPGD253 SSSGWTAGAA263 AYYVGYLQPR 273 TFLLKYNENG283 TITDAVDCAL293 DPLSETKCTL303 KSFTVEKGIY313 QTSNFRVQPT 323 ESIVRFPNIT333 NLCPFGEVFN343 ATRFASVYAW353 NRKRISNCVA363 DYSVLYNSAS 373 FSTFKCYGVS383 PTKLNDLCFT393 NVYADSFVIR403 GDEVRQIAPG413 QTGKIADYNY 423 KLPDDFTGCV433 IAWNSNNLDS443 KVGGNYNYLY453 RLFRKSNLKP463 FERDISTEIY 473 QAGSTPCNGV483 EGFNCYFPLQ493 SYGFQPTNGV503 GYQPYRVVVL513 SFELLHAPAT 523 VCGPKKSTNL533 VKNKCVNFNF543 NGLTGTGVLT553 ESNKKFLPFQ563 QFGRDIADTT 573 DAVRDPQTLE583 ILDITPCSFG593 GVSVITPGTN603 TSNQVAVLYQ613 DVNCTTWRVY 636 STGSNVFQTR646 AGCLIGAEHV656 NNSYECDIPI666 GAGICASYQT676 SQSIIAYTMS 698 LGAENSVAYS708 NNSIAIPTNF718 TISVTTEILP728 VSMTKTSVDC738 TMYICGDSTE 748 CSNLLLQYGS758 FCTQLNRALT768 GIAVEQDKNT778 QEVFAQVKQI788 YKTPPIKDFG 798 GFNFSQILPD808 PSKPSKRSFI818 EDLLFNKVTL828 ADAGFIKQYG838 DCLGDIAARD 848 LICAQKFNGL858 TVLPPLLTDE868 MIAQYTSALL878 AGTITSGWTF888 GAGAALQIPF 898 AMQMAYRFNG908 IGVTQNVLYE918 NQKLIANQFN928 SAIGKIQDSL938 SSTASALGKL 948 QDVVNQNAQA958 LNTLVKQLSS968 NFGAISSVLN978 DILSRLDKVE988 AEVQIDRLIT 998 GRLQSLQTYV1008 TQQLIRAAEI1018 RASANLAATK1028 MSECVLGQSK1038 RVDFCGKGYH 1048 LMSFPQSAPH1058 GVVFLHVTYV1068 PAQEKNFTTA1078 PAICHDGKAH1088 FPREGVFVSN 1098 GTHWFVTQRN1108 FYEPQIITTD1118 NTFVSGNCDV1128 VIGIVNNTVY1138 D |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SIA or .SIA2 or .SIA3 or :3SIA;style chemicals stick;color identity;select .A:145 or .A:152 or .A:181 or .A:183 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249 or .A:250 or .A:259; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Stearic acid | Ligand Info | |||||
| Structure Description | Locked Wuhan SARS-CoV2 Prefusion Spike ectodomain with lipid bound | PDB:7Z3Z | ||||
| Method | Electron microscopy | Resolution | 3.10 Å | Mutation | No | [3] |
| PDB Sequence |
QCVNLTTRTL
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHKRFD 80 NPVLPFNDGV90 YFASTEKSNI100 IRGWIFGTTL110 DSKTQSLLIV120 NNATNVVIKV 130 CEFQFCNDPF140 LGVYMESEFR158 VYSSANNCTF168 EYVSQPFLMD178 NFKNLREFVF 194 KNIDGYFKIY204 SKHTPINLVR214 DLPQGFSALE224 PLVDLPIGIN234 ITRFQTLLAL 244 HRSWLTPGDS254 SSGWTAGAAA264 YYVGYLQPRT274 FLLKYNENGT284 ITDAVDCALD 294 PLSETKCTLK304 SFTVEKGIYQ314 TSNFRVQPTE324 SIVRFPNITN334 LCPFGEVFNA 344 TRFASVYAWN354 RKRISNCVAD364 YSVLYNSASF374 STFKCYGVSP384 TKLNDLCFTN 394 VYADSFVIRG404 DEVRQIAPGQ414 TGKIADYNYK424 LPDDFTGCVI434 AWNSNNLDSK 444 VGGNYNYLYR454 LFRKSNLKPF464 ERDISTEIYQ474 AGSTPCNGVE484 GFNCYFPLQS 494 YGFQPTNGVG504 YQPYRVVVLS514 FELLHAPATV524 CGPKKSTNLV534 KNKCVNFNFN 544 GLTGTGVLTE554 SNKKFLPFQQ564 FGRDIADTTD574 AVRDPQTLEI584 LDITPCSFGG 594 VSVITPGTNT604 SNEVAVLYQD614 VNCTETWRVY636 STGSNVFQTR646 AGCLIGAEHV 656 NNSYECDIPI666 GAGICASYQT676 SQSIIAYTMS698 LGAENSVAYS708 NNSIAIPTNF 718 TISVTTEILP728 VSMTKTSVDC738 TMYICGDSTE748 CSNLLLQYGS758 FCTQLNRALT 768 GIAVEQDKNT778 QEVFAQVKQI788 YKTPPIKDFG798 GFNFSQILPD808 PSKPSKRSFI 818 EDLLFNKVTL828 ADAGFIKQYG838 DCLGDIAARD848 LICAQKFNGL858 TVLPPLLTDE 868 MIAQYTSALL878 AGTITSGWTF888 GAGAALQIPF898 AMQMAYRFNG908 IGVTQNVLYE 918 NQKLIANQFN928 SAIGKIQDSL938 SSTASALGKL948 QDVVNQNAQA958 LNTLVKQLSS 968 NFGAISSVLN978 DILSRLDPPE988 AEVQIDRLIT998 GRLQSLQTYV1008 TQQLIRAAEI 1018 RASANLAATK1028 MSECVLGQSK1038 RVDFCGKGYH1048 LMSFPQSAPH1058 GVVFLHVTYV 1068 PAQEKNFTTA1078 PAICHDGKAH1088 FPREGVFVSN1098 GTHWFVTQRN1108 FYEPQIITTD 1118 NTFVSGNCDV1128 VIGIVNNTVY1138 DPLQPELDS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .STE or .STE2 or .STE3 or :3STE;style chemicals stick;color identity;select .A:336 or .A:337 or .A:338 or .A:341 or .A:342 or .A:358 or .A:361 or .A:363 or .A:365 or .A:368 or .A:369 or .A:372 or .A:373 or .A:374 or .A:377 or .A:387 or .A:392 or .A:395 or .A:397 or .A:432 or .A:434 or .A:513 or .A:515 or .A:524; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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CYS336
2.623
PRO337
3.275
PHE338
2.259
VAL341
2.575
PHE342
3.290
ILE358
2.123
CYS361
4.810
ALA363
2.497
TYR365
2.297
LEU368
2.347
TYR369
2.077
ALA372
4.315
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| Ligand Name: Alpha-D-Mannose | Ligand Info | |||||
| Structure Description | Prototypic SARS-CoV-2 G614 spike (open form) | PDB:7TGX | ||||
| Method | Electron microscopy | Resolution | 3.20 Å | Mutation | Yes | [4] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHKRFD 80 NPVLPFNDGV90 YFASTEKSNI100 IRGWIFGTTL110 DSKTQSLLIV120 NNATNVVIKV 130 CEFQFCNDPF140 LGVYYHKNNK150 SWMESEFRVY160 SSANNCTFEY170 VSQPFLMDLE 180 GKQGNFKNLR190 EFVFKNIDGY200 FKIYSKHTPI210 NLVRDLPQGF220 SALEPLVDLP 230 IGINITRFQT240 LLALSSSGWT259 AGAAAYYVGY269 LQPRTFLLKY279 NENGTITDAV 289 DCALDPLSET299 KCTLKSFTVE309 KGIYQTSNFR319 VQPTESIVRF329 PNITNLCPFG 339 EVFNATRFAS349 VYAWNRKRIS359 NCVADYSVLY369 NSASFSTFKC379 YGVSPTKLND 389 LCFTNVYADS399 FVIRGDEVRQ409 IAPGQTGKIA419 DYNYKLPDDF429 TGCVIAWNSN 439 NLDSKVGGNY449 NYLYRLFRKS459 NLKPFERDIS469 TEIYQAGSTP479 CNGVEGFNCY 489 FPLQSYGFQP499 TNGVGYQPYR509 VVVLSFELLH519 APATVCGPKK529 STNLVKNKCV 539 NFNFNGLTGT549 GVLTESNKKF559 LPFQQFGRDI569 ADTTDAVRDP579 QTLEILDITP 589 CSFGGVSVIT599 PGTNTSNQVA609 VLYQGVNCTE619 VPVAITWRVY636 STGSNVFQTR 646 AGCLIGAEHV656 NNSYECDIPI666 GAGICASYQT676 SQSIIAYTMS698 LGAENSVAYS 708 NNSIAIPTNF718 TISVTTEILP728 VSMTKTSVDC738 TMYICGDSTE748 CSNLLLQYGS 758 FCTQLNRALT768 GIAVEQDKNT778 QEVFAQVKQI788 YKTPPIKDFG798 GFNFSQILPD 808 PSKPSKRSFI818 EDLLFNKVTL828 LICAQKFNGL858 TVLPPLLTDE868 MIAQYTSALL 878 AGTITSGWTF888 GAGAALQIPF898 AMQMAYRFNG908 IGVTQNVLYE918 NQKLIANQFN 928 SAIGKIQDSL938 SSTASALGKL948 QDVVNQNAQA958 LNTLVKQLSS968 NFGAISSVLN 978 DILSRLDPPE988 AEVQIDRLIT998 GRLQSLQTYV1008 TQQLIRAAEI1018 RASANLAATK 1028 MSECVLGQSK1038 RVDFCGKGYH1048 LMSFPQSAPH1058 GVVFLHVTYV1068 PAQEKNFTTA 1078 PAICHDGKAH1088 FPREGVFVSN1098 GTHWFVTQRN1108 FYEPQIITTD1118 NTFVSGNCDV 1128 VIGIVNNTVY1138 DPLQPELDSF1148 K
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MAN or .MAN2 or .MAN3 or :3MAN;style chemicals stick;color identity;select .C:716 or .C:717 or .C:718 or .C:922 or .C:1071; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Biliverdine Ix Alpha | Ligand Info | |||||
| Structure Description | Crystal structure of SARS-CoV-2 spike protein N-terminal domain in complex with biliverdin | PDB:7B62 | ||||
| Method | X-ray diffraction | Resolution | 1.82 Å | Mutation | No | [5] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVSGT 73 NGTKRFDNPV83 LPFNDGVYFA93 STEKSNIIRG103 WIFGTTLDSK113 TQSLLIVNNA 123 TNVVIKVCEF133 QFCNDPFLGV143 YYHKNNKSWM153 ESEFRVYSSA163 NNCTFEYVSQ 173 PFLMDLEGKQ183 GNFKNLREFV193 FKNIDGYFKI203 YSKHTPINLV213 RDLPQGFSAL 223 EPLVDLPIGI233 NITRFQTLLA243 LHRSYLTPGD253 SSSGWTAGAA263 AYYVGYLQPR 273 TFLLKYNENG283 TITDAVDCAL293 DPLSETKCTL303 KSFTVEKGSS313 GLEVLF |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BLA or .BLA2 or .BLA3 or :3BLA;style chemicals stick;color identity;select .A:99 or .A:101 or .A:102 or .A:103 or .A:104 or .A:119 or .A:120 or .A:121 or .A:126 or .A:177 or .A:188 or .A:190 or .A:192 or .A:203 or .A:207 or .A:226; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-alpha-L-xylo-hexofuranoside | Ligand Info | |||||
| Structure Description | Structure of SARS-CoV-2 3Q-2P full-length prefusion spike trimer (C3 symmetry) | PDB:7JJI | ||||
| Method | Electron microscopy | Resolution | 3.60 Å | Mutation | Yes | [6] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVSGT 73 NGTKRFDNPV83 LPFNDGVYFA93 STEKSNIIRG103 WIFGTTLDSK113 TQSLLIVNNA 123 TNVVIKVCEF133 QFCNDPFLGV143 YYHKNNKSWM153 ESEFRVYSSA163 NNCTFEYVSQ 173 PFLMDLEGKQ183 GNFKNLREFV193 FKNIDGYFKI203 YSKHTPINLV213 RDLPQGFSAL 223 EPLVDLPIGI233 NITRFQTLLA243 LHRSYLTPGD253 SSSGWTAGAA263 AYYVGYLQPR 273 TFLLKYNENG283 TITDAVDCAL293 DPLSETKCTL303 KSFTVEKGIY313 QTSNFRVQPT 323 ESIVRFPNIT333 NLCPFGEVFN343 ATRFASVYAW353 NRKRISNCVA363 DYSVLYNSAS 373 FSTFKCYGVS383 PTKLNDLCFT393 NVYADSFVIR403 GDEVRQIAPG413 QTGKIADYNY 423 KLPDDFTGCV433 IAWNSNNLDS443 KVGGNYNYLY453 RLFRKSNLKP463 FERDISTEIY 473 QAGSTPCNGV483 EGFNCYFPLQ493 SYGFQPTNGV503 GYQPYRVVVL513 SFELLHAPAT 523 VCGPKKSTNL533 VKNKCVNFNF543 NGLTGTGVLT553 ESNKKFLPFQ563 QFGRDIADTT 573 DAVRDPQTLE583 ILDITPCSFG593 GVSVITPGTN603 TSNQVAVLYQ613 DVNCTTWRVY 636 STGSNVFQTR646 AGCLIGAEHV656 NNSYECDIPI666 GAGICASYQT676 QSQSIIAYTM 697 SLGAENSVAY707 SNNSIAIPTN717 FTISVTTEIL727 PVSMTKTSVD737 CTMYICGDST 747 ECSNLLLQYG757 SFCTQLNRAL767 TGIAVEQDKN777 TQEVFAQVKQ787 IYKTPPIKDF 797 GGFNFSQILP807 DPSKPSKRSF817 IEDLLFNKVT827 LADAGFIKQY837 GDCLGDIAAR 847 DLICAQKFNG857 LTVLPPLLTD867 EMIAQYTSAL877 LAGTITSGWT887 FGAGAALQIP 897 FAMQMAYRFN907 GIGVTQNVLY917 ENQKLIANQF927 NSAIGKIQDS937 LSSTASALGK 947 LQDVVNQNAQ957 ALNTLVKQLS967 SNFGAISSVL977 NDILSRLDPP987 EAEVQIDRLI 997 TGRLQSLQTY1007 VTQQLIRAAE1017 IRASANLAAT1027 KMSECVLGQS1037 KRVDFCGKGY 1047 HLMSFPQSAP1057 HGVVFLHVTY1067 VPAQEKNFTT1077 APAICHDGKA1087 HFPREGVFVS 1097 NGTHWFVTQR1107 NFYEPQIITT1117 DNTFVSGNCD1127 VVIGIVNNTV1137 YDPLQPELD |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VCG or .VCG2 or .VCG3 or :3VCG;style chemicals stick;color identity;select .A:96 or .A:99 or .A:101 or .A:102 or .A:103 or .A:104 or .A:119 or .A:121 or .A:126 or .A:128 or .A:168 or .A:170 or .A:172 or .A:173 or .A:175 or .A:190 or .A:192 or .A:203 or .A:205 or .A:207 or .A:226 or .A:227 or .A:228 or .A:229 or .A:230; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLU96
4.942
ASN99
4.558
ILE101
3.274
ARG102
3.854
GLY103
3.835
TRP104
3.687
ILE119
3.666
ASN121
2.717
VAL126
3.478
ILE128
3.878
PHE168
3.740
TYR170
3.455
SER172
3.469
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| Ligand Name: alpha-L-Fucose | Ligand Info | |||||
| Structure Description | Structure of the SARS-CoV-2 spike glycoprotein in complex with the 47D11 neutralizing antibody Fab fragment | PDB:7AKD | ||||
| Method | Electron microscopy | Resolution | 4.00 Å | Mutation | No | [7] |
| PDB Sequence |
AYTNSFTRGV
36 YYPDKVFRSS46 VLHSTQDLFL56 PFFSNVTWFH66 NPVLPFNDGV90 YFASTEKSNI 100 IRGWIFGTTL110 DSKTQSLLIV120 NNATNVVIKV130 CEFQFCNDPF140 NNCTFEYVSF 186 KNLREFVFKN196 YFKIYSKHTP209 INLVRDLPQG219 FSALEPLVDL229 PIGINITRFQ 239 TLLAAYYVGY269 LQPRTFLLKY279 NENGTITDAV289 DCALDPLSET299 KCTLKSFTVE 309 KGIYQTSNFR319 VQPTESIVRF329 PNITNLCPFG339 EVFNATRFAS349 VYAWNRKRIS 359 NCVADYSVLY369 NSASFSTFKC379 YGVSPTKLND389 LCFTNVYADS399 FVIRGDEVRQ 409 IAPGQTGKIA419 DYNYKLPDDF429 TGCVIAWNSN439 NLDSKVGGNY449 NYLYRLFRKS 459 NLKPFERDIS469 TPLQSYGFQP499 TNGVGYQPYR509 VVVLSFELLH519 APATVCGPKK 529 STNLVKNKCV539 NFNFNGLTGT549 GVLTESNKKF559 LPFQQFGRDI569 ADTTDAVRDP 579 QTLEILDITP589 CSFGGVSVIT599 PGTNTSNQVA609 VLYQDVNCTE619 VNVFQTRAGC 649 LIGAEHVNNS659 YECDIPIGAG669 ICASYQTSQS691 IIAYTMSLGA701 ENSVAYSNNS 711 IAIPTNFTIS721 VTTEILPVSM731 TKTSVDCTMY741 ICGDSTECSN751 LLLQYGSFCT 761 QLNRALTGIA771 VEQDKNTQEV781 FAQVKQIYKT791 PPIKDFGGFN801 FSQILPDPSK 811 PSKRSFIEDL821 LFNKVTKFNG857 LTVLPPLLTD867 EMIAQYTSAL877 LAGTITSGWT 887 FGAGAALQIP897 FAMQMAYRFN907 GIGVTQNVLY917 ENQKLIANQF927 NSAIGKIQDS 937 LSSTASALGK947 LQDVVNQNAQ957 ALNTLVKQLS967 SNFGAISSVL977 NDILSRLDPP 987 EAEVQIDRLI997 TGRLQSLQTY1007 VTQQLIRAAE1017 IRASANLAAT1027 KMSECVLGQS 1037 KRVDFCGKGY1047 HLMSFPQSAP1057 HGVVFLHVTY1067 VPAQEKNFTT1077 APAICHDGKA 1087 HFPREGVFVS1097 NGTHWFVTQR1107 NFYEPQIITT1117 DNTFVSGNCD1127 VVIGIVNNTV 1137 YDPLQPELDS1147
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FUC or .FUC2 or .FUC3 or :3FUC;style chemicals stick;color identity;select .A:1074; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2,3,5-Triiodobenzamide | Ligand Info | |||||
| Structure Description | SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C3 symmetry | PDB:7QUR | ||||
| Method | Electron microscopy | Resolution | 2.27 Å | Mutation | Yes | [2] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVSGT 73 NGTKRFDNPV83 LPFNDGVYFA93 STEKSNIIRG103 WIFGTTLDSK113 TQSLLIVNNA 123 TNVVIKVCEF133 QFCNDPFLGV143 YYHKNNKSWM153 ESEFRVYSSA163 NNCTFEYVSQ 173 PFLMDLEGKQ183 GNFKNLREFV193 FKNIDGYFKI203 YSKHTPINLV213 RDLPQGFSAL 223 EPLVDLPIGI233 NITRFQTLLA243 LHRSYLTPGD253 SSSGWTAGAA263 AYYVGYLQPR 273 TFLLKYNENG283 TITDAVDCAL293 DPLSETKCTL303 KSFTVEKGIY313 QTSNFRVQPT 323 ESIVRFPNIT333 NLCPFGEVFN343 ATRFASVYAW353 NRKRISNCVA363 DYSVLYNSAS 373 FSTFKCYGVS383 PTKLNDLCFT393 NVYADSFVIR403 GDEVRQIAPG413 QTGKIADYNY 423 KLPDDFTGCV433 IAWNSNNLDS443 KVGGNYNYLY453 RLFRKSNLKP463 FERDISTEIY 473 QAGSTPCNGV483 EGFNCYFPLQ493 SYGFQPTNGV503 GYQPYRVVVL513 SFELLHAPAT 523 VCGPKKSTNL533 VKNKCVNFNF543 NGLTGTGVLT553 ESNKKFLPFQ563 QFGRDIADTT 573 DAVRDPQTLE583 ILDITPCSFG593 GVSVITPGTN603 TSNQVAVLYQ613 DVNCTTWRVY 636 STGSNVFQTR646 AGCLIGAEHV656 NNSYECDIPI666 GAGICASYQT676 SQSIIAYTMS 698 LGAENSVAYS708 NNSIAIPTNF718 TISVTTEILP728 VSMTKTSVDC738 TMYICGDSTE 748 CSNLLLQYGS758 FCTQLNRALT768 GIAVEQDKNT778 QEVFAQVKQI788 YKTPPIKDFG 798 GFNFSQILPD808 PSKPSKRSFI818 EDLLFNKVTL828 ADAGFIKQYG838 DCLGDIAARD 848 LICAQKFNGL858 TVLPPLLTDE868 MIAQYTSALL878 AGTITSGWTF888 GAGAALQIPF 898 AMQMAYRFNG908 IGVTQNVLYE918 NQKLIANQFN928 SAIGKIQDSL938 SSTASALGKL 948 QDVVNQNAQA958 LNTLVKQLSS968 NFGAISSVLN978 DILSRLDKVE988 AEVQIDRLIT 998 GRLQSLQTYV1008 TQQLIRAAEI1018 RASANLAATK1028 MSECVLGQSK1038 RVDFCGKGYH 1048 LMSFPQSAPH1058 GVVFLHVTYV1068 PAQEKNFTTA1078 PAICHDGKAH1088 FPREGVFVSN 1098 GTHWFVTQRN1108 FYEPQIITTD1118 NTFVSGNCDV1128 VIGIVNNTVY1138 D |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GE9 or .GE92 or .GE93 or :3GE9;style chemicals stick;color identity;select .A:656 or .A:660 or .A:661 or .A:673 or .A:675 or .A:693 or .A:695; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-[2-[[3-(2-carboxyethyl)-5-[(3-ethyl-4-methyl-5-oxopyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-2-yl]methyl]-5-[(4-ethyl-3-methyl-5-oxopyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid | Ligand Info | |||||
| Structure Description | CryoEM structure of SARS-CoV-2 spike monomer in complex with neutralising antibody P008_60 | PDB:7ZBU | ||||
| Method | Electron microscopy | Resolution | 4.31 Å | Mutation | Yes | [8] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVSGT 73 NGTKRFDNPV83 LPFNDGVYFA93 STEKSNIIRG103 WIFGTTLDSK113 TQSLLIVNNA 123 TNVVIKVCEF133 QFCNDPFLGV143 YYHKNNKSWM153 ESEFRVYSSA163 NNCTFEYVSQ 173 PFLMDLEGKQ183 GNFKNLREFV193 FKNIDGYFKI203 YSKHTPINLV213 RDLPQGFSAL 223 EPLVDLPIGI233 NITRFQTLLA243 LHRSYLTPGD253 SSSGWTAGAA263 AYYVGYLQPR 273 TFLLKYNENG283 TITDAVDCAL293 DPLSETKCTL303 KSFTVEKGIY313 QTSNFRVQPT 323 ESIVRFPNIT333 NLCPFGEVFN343 ATRFASVYAW353 NRKRISNCVA363 DYSVLYNSAS 373 FSTFKCYGVS383 PTKLNDLCFT393 NVYADSFVIR403 GDEVRQIAPG413 QTGKIADYNY 423 KLPDDFTGCV433 IAWNSNNLDS443 KVGGNYNYLY453 RLFRKSNLKP463 FERDISTEIY 473 QAGSTPCNGV483 EGFNCYFPLQ493 SYGFQPTNGV503 GYQPYRVVVL513 SFELLHAPAT 523 VCGPKKSTNL533 VKNKCVNFNF543 NGLTGTGVLT553 ESNKKFLPFQ563 QFGRDIADTT 573 DAVRDPQTLE583 ILDITPCSFG593 GVSVITPGTN603 TSNQVAVLYQ613 DVNCTEVPVV 635 YSTGSNVFQT645 RAGCLIGAEH655 VNNSYECDIP665 IGAGICASYQ675 TSQSIIAYTM 697
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3Q9 or .3Q92 or .3Q93 or :33Q9;style chemicals stick;color identity;select .A:99 or .A:101 or .A:102 or .A:103 or .A:104 or .A:119 or .A:121 or .A:126 or .A:177 or .A:190 or .A:192 or .A:203 or .A:205 or .A:207 or .A:226; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Xylitol | Ligand Info | |||||
| Structure Description | Crystal structure of SARS-CoV-2 S NTD bound to S2M28 Fab | PDB:7LY3 | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | No | [9] |
| PDB Sequence |
GTQCVNLTTR
21 TQLPPAYTNS31 FTRGVYYPDK41 VFRSSVLHST51 QDLFLPFFSN61 VTWFHAIHVS 71 NGTKRFDNPV83 LPFNDGVYFA93 STEKSNIIRG103 WIFGTTLDSK113 TQSLLIVNNA 123 TNVVIKVCEF133 QFCNDPFLGV143 YYHKNNKSWM153 ESEFRVYSSA163 NNCTFEYVSQ 173 PFLMDKNLRE191 FVFKNIDGYF201 KIYSKHTPIN211 LVRDLPQGFS221 ALEPLVDLPI 231 GINITRFQTL241 LALHRSYLTP251 GDSSSGWTAG261 AAAYYVGYLQ271 PRTFLLKYNE 281 NGTITDAVDC291 ALDPLSETKC301 TAKS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .XYL or .XYL2 or .XYL3 or :3XYL;style chemicals stick;color identity;select .A:38 or .A:40 or .A:41 or .A:42 or .A:43 or .A:224 or .A:225 or .A:283; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-(acetylamino)-1,5-anhydro-2-deoxy-D-mannitol | Ligand Info | |||||
| Structure Description | SARS-CoV-2 Spike RBD (dimer) in complex with two Fu2 nanobodies | PDB:7NLL | ||||
| Method | Electron microscopy | Resolution | 2.89 Å | Mutation | No | [10] |
| PDB Sequence |
TNLCPFGEVF
342 NATRFASVYA352 WNRKRISNCV362 ADYSVLYNSA372 SFSTFKCYGV382 SPTKLNDLCF 392 TNVYADSFVI402 RGDEVRQIAP412 GQTGKIADYN422 YKLPDDFTGC432 VIAWNSNNLD 442 SKVGGNYNYL452 YRLFRKSNLK462 PFERDISTEI472 YQAGSTPCNG482 VEGFNCYFPL 492 QSYGFQPTNG502 VGYQPYRVVV512 LSFELLHAPA522 TVCGPK
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .RTV or .RTV2 or .RTV3 or :3RTV;style chemicals stick;color identity;select .B:339 or .B:343; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1-Propanol | Ligand Info | |||||
| Structure Description | SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2X35 Fab and S309 Fab | PDB:7R6W | ||||
| Method | X-ray diffraction | Resolution | 1.83 Å | Mutation | No | [11] |
| PDB Sequence |
TNLCPFGEVF
342 NATRFASVYA352 WNRKRISNCV362 ADYSVLYNSA372 SFSTFKCYGV382 SPTKLNDLCF 392 TNVYADSFVI402 RGDEVRQIAP412 GQTGKIADYN422 YKLPDDFTGC432 VIAWNSNNLD 442 SKVGGNYNYL452 YRLFRKSNLK462 PFERDISTEI472 YQAGSTPCNG482 VEGFNCYFPL 492 QSYGFQPTNG502 VGYQPYRVVV512 LSFELLHAPA522 TVCGP
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .POL or .POL2 or .POL3 or :3POL;style chemicals stick;color identity;select .R:372 or .R:373 or .R:374 or .R:375 or .R:435 or .R:436 or .R:437 or .R:503 or .R:508; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1,3-Butanediol | Ligand Info | |||||
| Structure Description | Structure of sybody MR17-SR31 fusion in complex with the SARS-CoV-2 S Receptor Binding domain (RBD) | PDB:7D30 | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [12] |
| PDB Sequence |
NLCPFGEVFN
343 ATRFASVYAW353 NRKRISNCVA363 DYSVLYNSAS373 FSTFKCYGVS383 PTKLNDLCFT 393 NVYADSFVIR403 GDEVRQIAPG413 QTGKIADYNY423 KLPDDFTGCV433 IAWNSNNLDS 443 KVGGNYNYLY453 RLFRKSNLKP463 FERDISTEIY473 QAGSTPCNGV483 EGFNCYFPLQ 493 SYGFQPTNGV503 GYQPYRVVVL513 SFELLHAPAT523 VCGGTLEVLF538 Q |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BU2 or .BU22 or .BU23 or :3BU2;style chemicals stick;color identity;select .B:456 or .B:475 or .B:487 or .B:489 or .B:499 or .B:500 or .B:501 or .B:502 or .B:506; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | A Retinol Derivative Inhibits SARS-CoV-2 Infection by Interrupting Spike-Mediated Cellular Entry. mBio. 2022 Aug 30;13(4):e0148522. | ||||
| REF 2 | Pathogen-sugar interactions revealed by universal saturation transfer analysis. Science. 2022 Jul 22;377(6604):eabm3125. | ||||
| REF 3 | The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer. doi:10.1101/2020.08.13.249177. | ||||
| REF 4 | Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain. Nat Commun. 2022 Mar 3;13(1):1214. | ||||
| REF 5 | SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity. Sci Adv. 2021 May 28;7(22):eabg7607. | ||||
| REF 6 | Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate. Science. 2020 Nov 27;370(6520):1089-1094. | ||||
| REF 7 | Structural insights into the cross-neutralization of SARS-CoV and SARS-CoV-2 by the human monoclonal antibody 47D11. Sci Adv. 2021 Jun 2;7(23):eabf5632. | ||||
| REF 8 | A neutralizing epitope on the SD1 domain of SARS-CoV-2 spike targeted following infection and vaccination. Cell Rep. 2022 Aug 23;40(8):111276. | ||||
| REF 9 | N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell. 2021 Apr 29;184(9):2332-2347.e16. | ||||
| REF 10 | A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Nat Commun. 2022 Jan 10;13(1):155. | ||||
| REF 11 | SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Nature. 2021 Sep;597(7874):97-102. | ||||
| REF 12 | A high-affinity RBD-targeting nanobody improves fusion partner's potency against SARS-CoV-2. PLoS Pathog. 2021 Mar 3;17(3):e1009328. | ||||
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