Structure of PDB 7jji Chain C Binding Site BS03

Receptor Information
>7jji Chain C (length=1109) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVT
WFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSK
TQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSA
NNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLV
RDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAA
AYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIY
QTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVA
DYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPG
QTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKP
FERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVL
SFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQ
QFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQ
DVNCTTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQT
QSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVD
CTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQ
IYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQY
GDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWT
FGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDS
LSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPP
EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQS
KRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKA
HFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTV
YDPLQPELD
Ligand information
Ligand IDVCG
InChIInChI=1S/C32H60O10/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-30(36)40-25-24-37-27-29(39-22-19-34)32-28(38-21-18-33)26-31(42-32)41-23-20-35/h9-10,28-29,31-35H,2-8,11-27H2,1H3/b10-9+/t28-,29+,31-,32+/m1/s1
InChIKeyRGPBUVUVZKQNHD-YPJAPDKZSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(CC(OCCOCC(OCCO)C1C(OCCO)CC(O1)OCCO)=O)CCCCC[C@H]=[C@H]CCCCCCCC
CACTVS 3.385CCCCCCCC\C=C\CCCCCCCC(=O)OCCOC[C@H](OCCO)[C@H]1O[C@H](C[C@H]1OCCO)OCCO
CACTVS 3.385CCCCCCCCC=CCCCCCCCC(=O)OCCOC[CH](OCCO)[CH]1O[CH](C[CH]1OCCO)OCCO
OpenEye OEToolkits 2.0.7CCCCCCCCC=CCCCCCCCC(=O)OCCOCC(C1C(CC(O1)OCCO)OCCO)OCCO
OpenEye OEToolkits 2.0.7CCCCCCCC/C=C/CCCCCCCC(=O)OCCOC[C@@H]([C@@H]1[C@@H](C[C@@H](O1)OCCO)OCCO)OCCO
FormulaC32 H60 O10
Name2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-alpha-L-xylo-hexofuranoside;
Polysorbate 80
ChEMBL
DrugBank
ZINCZINC000008101168
PDB chain7jji Chain C Residue 1503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7jji Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		N121 V126 Y170 R190 H207
Binding residue
(residue number reindexed from 1)		N108 V113 Y157 R177 H194
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0019064 fusion of virus membrane with host plasma membrane
GO:0039654 fusion of virus membrane with host endosome membrane
GO:0046813 receptor-mediated virion attachment to host cell
GO:0075509 endocytosis involved in viral entry into host cell
Cellular Component
GO:0016020 membrane
GO:0019031 viral envelope
GO:0055036 virion membrane

View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7jji, PDBe:7jji, PDBj:7jji
PDBsum7jji
PubMed33082295
UniProtP0DTC2|SPIKE_SARS2 Spike glycoprotein (Gene Name=S)

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