Structure of PDB 6zoz Chain C Binding Site BS01

Receptor Information
>6zoz Chain C (length=1070) 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
FHAIHDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNAT
NVVIKVCEFQFCNDPFLGMESEFRVYSSANNCTFEYVSQPFLGNFKNLRE
FVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTL
LALAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTV
EKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRI
SNCVADYSVLYNSASFSTFKCYGVCPTKLNDLCFTNVYADSFVIRGDEVR
QIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRK
SNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPY
RVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKK
FLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQV
AVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNN
SYECDIPIGAGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGI
AVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIED
LLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMI
AQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQ
KLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNF
GAISSVLNDILSRLCPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPA
QEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT
FVSGNCDVVIGIVNNTVYDP
Ligand information
Ligand IDBLA
InChIInChI=1S/C33H34N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-15,34H,1-2,9-12H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14-,29-15-
InChIKeyGWZYPXHJIZCRAJ-SRVCBVSDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c([nH]c1\C=C/2\C(=C(C(=O)N2)C=C)C)\C=C/3\C(=C(C(=N3)\C=C/4\C(=C(C(=O)N4)C)C=C)C)CCC(=O)O)CCC(=O)O
OpenEye OEToolkits 1.5.0Cc1c(c([nH]c1C=C2C(=C(C(=O)N2)C=C)C)C=C3C(=C(C(=N3)C=C4C(=C(C(=O)N4)C)C=C)C)CCC(=O)O)CCC(=O)O
CACTVS 3.341Cc1c([nH]c(C=C2N=C(C=C3NC(=O)C(=C3C=C)C)C(=C2CCC(O)=O)C)c1CCC(O)=O)C=C4NC(=O)C(=C4C)C=C
CACTVS 3.341Cc1c([nH]c(\C=C2/N=C(\C=C3/NC(=O)C(=C3C=C)C)C(=C2CCC(O)=O)C)c1CCC(O)=O)\C=C4/NC(=O)C(=C4C)C=C
FormulaC33 H34 N4 O6
NameBILIVERDINE IX ALPHA
ChEMBL
DrugBank
ZINCZINC000103534374
PDB chain6zoz Chain C Residue 1314 [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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PDB6zoz A thermostable, closed SARS-CoV-2 spike protein trimer.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		N99 I101 I119 N121 V126 R190 F192
Binding residue
(residue number reindexed from 1)		N75 I77 I95 N97 V102 R149 F151
Annotation score4
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6zoz, PDBe:6zoz, PDBj:6zoz
PDBsum6zoz
PubMed32737467
UniProtP0DTC2|SPIKE_SARS2 Spike glycoprotein (Gene Name=S)

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