Structure of PDB 7e7b Chain B Binding Site BS02

Receptor Information
>7e7b Chain B (length=1102) Species: 9606,2697049 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVT
WFHAIHVTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLL
IVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTF
EYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQ
GFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVG
YLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNF
RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVL
YNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKI
ADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDI
STEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELL
HAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRD
IADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCW
RVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAY
TMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGD
STECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIK
DFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIA
ARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQ
IPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASAL
GKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDR
LITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGK
GYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVF
VSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPEL
DS
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 chain7e7b Chain A Residue 1609 [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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PDB7e7b Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		V126 F168 Y170 F192 I203 V227 P230
Binding residue
(residue number reindexed from 1)		V108 F150 Y152 F174 I185 V209 P212
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005201 extracellular matrix structural constituent
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

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7e7b, PDBe:7e7b, PDBj:7e7b
PDBsum7e7b
PubMed33692215
UniProtP02452|CO1A1_HUMAN Collagen alpha-1(I) chain (Gene Name=COL1A1);
P0DTC2|SPIKE_SARS2 Spike glycoprotein (Gene Name=S)

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