Structure of PDB 8opm Chain A Binding Site BS01

Receptor Information
>8opm Chain A (length=1194) Species: 290028,559292 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VIGDFNCTNFAINDLNTTIPRISEYVVDVSYGLGTYYILDRVYLNTTILF
TGYFPKSGANFRDLSLKGTTKLSTLWYQKPFLSDFNNGIFSRVKNTKLYV
NKTLYSEFSTIVIGSVFINNSYTIVVQPHNGVLEITACQYTMCEYPHTIC
KSIGSSRNESWHFDKSEPLCLFKKNFTYNVSTDWLYFHFYQERGTFYAYY
ADSGMPTTFLFSLYLGTLLSHYYVLPLTCNAISSNTDNETLQYWVTPLSK
RQYLLKFDDRGVITNAVDCSSSFFSEIQCKTKSLLPNTGVYDLSGFTVKP
VATVHRRIPDLPDCDIDKWLNNFNVPSPLNWERKIFSNCNFNLSTLLRLV
HTDSFSCNNFDESKIYGSCFKSIVLDKFAIPNSRRSDLQLGSSGFLQSSN
YKIDTTSSSCQLYYSLPAINVTINNYNPSSWNRRYGFNNFNLSSHSVVYS
RYCFSVNNTFCPCAKPSFASSCKSHKPPSASCPIGTNYRSCESTTVLDHT
DWCRCSCLPDPITAYDPRSCSQKKSLVGVGEHCAGFGVDEEKCGVLDGSY
NVSCLCSTDAFLGWSYDTCVSNNRCNIFSNFILNGINSGTTCSNDLLQPN
TEVFTDVCVDYDLYGITGQGIFKEVSAVYYNSWQNLLYDFNGNIIGFKDF
VTNKTYNIFPCYAGRVSAAFHQNASSLALLYRNLKCSYVLNNISLATQPY
FDSYLGCVFNADNLTDYSVSSCALRMGSGFCVDYNSYRFVTFEPFNVSFV
NDSIESVGGLYEIKIPTNFTIVGQEEFIQTNSPKVTIDCSLFVCSNYAAC
HDLLSEYGTFCDNINSILDEVNGLLDTTQLHVADTLMQGVTLSSNLNTNL
HFDVDNINFKSLVGCLGPHCGSSSRSFFEDLLFDKVKLSDVGFVEAYNNC
TGGSEIRDLLCVQSFNGIKVLPPILSESQISGYTTAATVAAMFPPWSAAA
GIPFSLNVQYRINGLGVTMDVLNKNQKLIATAFNNALLSIQNGFSATNSA
LAKIQSVVNSNAQALNSLLQQLFNKFGAISSSLQEILSRLDALEAQVQID
RLINGRLTALNAYVSQQLSDISLVKLGAALAMEKVNECVKSQSPRINFCG
NGNHILSLVQNAPYGLLFMHFSYKPISFKTVLVSPGLCISGDVGIAPKQG
YFIKHNDHWMFTGSSYYYPEPISDKNVVFMNTCSVNFTKAPLVY
Ligand information
Ligand IDSIA
InChIInChI=1S/C11H19NO9/c1-4(14)12-7-5(15)2-11(20,10(18)19)21-9(7)8(17)6(16)3-13/h5-9,13,15-17,20H,2-3H2,1H3,(H,12,14)(H,18,19)/t5-,6+,7+,8+,9+,11+/m0/s1
InChIKeySQVRNKJHWKZAKO-YRMXFSIDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(=O)N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O
OpenEye OEToolkits 1.5.0CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)O)O
OpenEye OEToolkits 1.5.0CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](CO)O)O)(C(=O)O)O)O
ACDLabs 10.04O=C(O)C1(O)OC(C(O)C(O)CO)C(NC(=O)C)C(O)C1
CACTVS 3.341CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
FormulaC11 H19 N O9
NameN-acetyl-alpha-neuraminic acid;
N-acetylneuraminic acid;
sialic acid;
alpha-sialic acid;
O-SIALIC ACID
ChEMBLCHEMBL1234621
DrugBankDB03721
ZINCZINC000004081651
PDB chain8opm Chain O Residue 1 [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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PDB8opm Sialoglycan binding triggers spike opening in a human coronavirus
Resolution3.7 Å
Binding residue
(original residue number in PDB)		T82 T83 S246
Binding residue
(residue number reindexed from 1)		T69 T70 S233
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003700 DNA-binding transcription factor activity
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0019062 virion attachment to host cell
GO:0019064 fusion of virus membrane with host plasma membrane
GO:0039654 fusion of virus membrane with host endosome membrane
GO:0046718 symbiont entry into host cell
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:0020002 host cell plasma membrane
GO:0044173 host cell endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0055036 virion membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8opm, PDBe:8opm, PDBj:8opm
PDBsum8opm
PubMed37794193
UniProtE0YJ44;
P03069|GCN4_YEAST General control transcription factor GCN4 (Gene Name=GCN4)

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