Structure of PDB 8p9y Chain C Binding Site BS01

Receptor Information
>8p9y Chain C (length=1076) 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]
CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTW
FHAIHVTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLI
VNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFE
YVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQG
FSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGY
LQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFR
VQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLY
NSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIA
DYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDIS
TEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLH
APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDI
ADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTE
VPNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTSQSIIAYTMSLG
AENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECS
NLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF
NFSQILPDPSKPSKRSFIEDLLFNKVTLADCAQKFNGLTVLPPLLTDEMI
AQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQ
KLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNF
GAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPA
QEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT
FVSGNCDVVIGIVNNTVYDPLQPELD
Ligand information
Ligand IDXIO
InChIInChI=1S/C63H59N11O16S3/c64-34-56(78)71-63(28-25-53(75)65-50(60(79)80)31-44-41-7-1-4-10-47(41)68-57(44)91-38-19-13-35(14-20-38)72(85)86,29-26-54(76)66-51(61(81)82)32-45-42-8-2-5-11-48(42)69-58(45)92-39-21-15-36(16-22-39)73(87)88)30-27-55(77)67-52(62(83)84)33-46-43-9-3-6-12-49(43)70-59(46)93-40-23-17-37(18-24-40)74(89)90/h1-24,50-52,68-70H,25-34,64H2,(H,65,75)(H,66,76)(H,67,77)(H,71,78)(H,79,80)(H,81,82)(H,83,84)/t50-,51-,52-/m0/s1
InChIKeyOJDYQRNEDPEFMJ-VPMCDZTMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc2c(c1)c(c([nH]2)Sc3ccc(cc3)[N+](=O)[O-])C[C@@H](C(=O)O)NC(=O)CCC(CCC(=O)N[C@@H](Cc4c5ccccc5[nH]c4Sc6ccc(cc6)[N+](=O)[O-])C(=O)O)(CCC(=O)N[C@@H](Cc7c8ccccc8[nH]c7Sc9ccc(cc9)[N+](=O)[O-])C(=O)O)NC(=O)CN
CACTVS 3.385NCC(=O)N[C](CCC(=O)N[CH](Cc1c([nH]c2ccccc12)Sc3ccc(cc3)[N+]([O-])=O)C(O)=O)(CCC(=O)N[CH](Cc4c([nH]c5ccccc45)Sc6ccc(cc6)[N+]([O-])=O)C(O)=O)CCC(=O)N[CH](Cc7c([nH]c8ccccc78)Sc9ccc(cc9)[N+]([O-])=O)C(O)=O
CACTVS 3.385NCC(=O)N[C@](CCC(=O)N[C@@H](Cc1c([nH]c2ccccc12)Sc3ccc(cc3)[N+]([O-])=O)C(O)=O)(CCC(=O)N[C@@H](Cc4c([nH]c5ccccc45)Sc6ccc(cc6)[N+]([O-])=O)C(O)=O)CCC(=O)N[C@@H](Cc7c([nH]c8ccccc78)Sc9ccc(cc9)[N+]([O-])=O)C(O)=O
OpenEye OEToolkits 2.0.7c1ccc2c(c1)c(c([nH]2)Sc3ccc(cc3)[N+](=O)[O-])CC(C(=O)O)NC(=O)CCC(CCC(=O)NC(Cc4c5ccccc5[nH]c4Sc6ccc(cc6)[N+](=O)[O-])C(=O)O)(CCC(=O)NC(Cc7c8ccccc8[nH]c7Sc9ccc(cc9)[N+](=O)[O-])C(=O)O)NC(=O)CN
FormulaC63 H59 N11 O16 S3
Name[(2~{S})-2-[[4-(2-azanylethanoylamino)-7-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-4-[3-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-3-oxidanylidene-propyl]-7-oxidanylidene-heptanoyl]amino]-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]propanoyl]oxysodium
ChEMBL
DrugBank
ZINC
PDB chain8p9y Chain C Residue 1307 [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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PDB8p9y C-2 Thiophenyl Tryptophan Trimers Inhibit Cellular Entry of SARS-CoV-2 through Interaction with the Viral Spike (S) Protein.
Resolution4.3 Å
Binding residue
(original residue number in PDB)		T478 F486 N487
Binding residue
(residue number reindexed from 1)		T459 F467 N468
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0039660 structural constituent of virion
GO:0042802 identical protein binding
GO:0046789 host cell surface receptor binding
GO:0048018 receptor ligand activity
Biological Process
GO:0007165 signal transduction
GO:0019062 virion attachment to host cell
GO:0019064 fusion of virus membrane with host plasma membrane
GO:0019081 viral translation
GO:0039587 suppression by virus of host tetherin activity
GO:0039654 fusion of virus membrane with host endosome membrane
GO:0046598 positive regulation of viral entry into host cell
GO:0046718 symbiont entry into host cell
GO:0046813 receptor-mediated virion attachment to host cell
GO:0052170 symbiont-mediated suppression of host innate immune response
GO:0061025 membrane fusion
GO:0075509 endocytosis involved in viral entry into host cell
GO:0098670 entry receptor-mediated virion attachment to host cell
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0019031 viral envelope
GO:0020002 host cell plasma membrane
GO:0043655 host extracellular space
GO:0044173 host cell endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0044228 host cell surface
GO:0055036 virion membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8p9y, PDBe:8p9y, PDBj:8p9y
PDBsum8p9y
PubMed37471688
UniProtP0DTC2|SPIKE_SARS2 Spike glycoprotein (Gene Name=S)

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