BioLiP

Receptor Information

>8y8b Chain A (length=271) Species: 443241 (Human coronavirus HKU1 (isolate N5)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

VIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTTLLF
TGYFPKSGANFRDLALKGSIYLSTLWYKPPFLSDFNNGIFSKVKNTKLYV
NNTLYSEFSTIVIGSVFVNTSYTIVVQPHNGILEITACQYTMCEYPHTVC
KSKGSIRNESWHIDSSEPLCLFKKNFTYNVSADWLYFHFYQERGVFYAYY
ADVGMPTTFLFSLYLGTILSHYYVMPLTCNAISSNTDNETLEYWVTPLSR
RQYLLNFDEHGVITNAVDCSS

Ligand ID

MJJ

InChI

InChI=1S/C14H23NO10/c1-6(16)15-10-8(18)4-14(23-3,13(21)22)25-12(10)11(20)9(19)5-24-7(2)17/h8-12,18-20H,4-5H2,1-3H3,(H,15,16)(H,21,22)/t8-,9+,10+,11+,12+,14+/m0/s1

InChIKey

NIEBVOWRRSQMQG-KXEMTNKZSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.7	CC(=O)NC1C(CC(OC1C(C(COC(=O)C)O)O)(C(=O)O)OC)O
CACTVS 3.385	CO[C]1(C[CH](O)[CH](NC(C)=O)[CH](O1)[CH](O)[CH](O)COC(C)=O)C(O)=O
CACTVS 3.385	CO[C@@]1(C[C@H](O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)COC(C)=O)C(O)=O
OpenEye OEToolkits 2.0.7	CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](COC(=O)C)O)O)(C(=O)O)OC)O
ACDLabs 12.01	OC1C(NC(C)=O)C(OC(C1)(C(O)=O)OC)C(C(O)COC(=O)C)O

Formula

C14 H23 N O10

Name

methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid;
methyl 9-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid;
methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid;
methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosidonic acid;
methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosidonic acid

PDB chain

8y8b Chain A Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	8y8b TMPRSS2 and glycan receptors synergistically facilitate coronavirus entry.
Resolution	3.01 Å
Binding residue (original residue number in PDB)	N26 Y28 L79 K80 S82 Y84 W89 S246
Binding residue (residue number reindexed from 1)	N13 Y15 L66 K67 S69 Y71 W76 S233
Annotation score	1

	Molecular Function
GO:0042802	identical protein binding

	Biological Process
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

PDB	RCSB:8y8b, PDBe:8y8b, PDBj:8y8b
PDBsum	8y8b
PubMed	38964329
UniProt	Q0ZME7\|SPIKE_CVHN5 Spike glycoprotein (Gene Name=S)

[Back to BioLiP]

Structure of PDB 8y8b Chain A Binding Site BS01