Structure of PDB 6q04 Chain B Binding Site BS02

Receptor Information
>6q04 Chain B (length=1159) Species: 1235996 (Human betacoronavirus 2c EMC/2012) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TVDVGPDSVKSACIEVDIQQTFFDKTWPRPIDVSKADGIIYPQGRTYSNI
TITYQGLFPYQGDHGDMYVYSAGHATGTTPQKLFVANYSQDVKQFANGFV
VRIGAAANSTGTVIISPSTSATIRKIYPAFMLGSSVGNFSDGKMGRFFNH
TLVLLPDGCGTLLRAFYCILEPRSGNHCPAGNSYTSFATYHTPATDCSDG
NYNRNASLNSFKEYFNLRNCTFMYTYNITEDEILEWFGITQTAQGVHLFS
SRYVDLYGGNMFQFATLPVYDTIKYYSIIPHSIRSIQSDRKAWAAFYVYK
LQPLTFLLDFSVDGYIRRAIDCGFNDLSQLHCSYESFDVESGVYSVSSFE
AKPSGSVVEQAEGVECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSL
FSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQF
NYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQL
VNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQL
QMGFGITVQYGTDTNSVCPKLEFANDTKIASQLGNCVEYSLYGVSGRGVF
QNCTAVGVRQQRFVYDAYQNLVGYYSDDGNYYCLRACVSVPVSVIYDKET
KTHATLFGSVACEHIYGPLQTPVGCVLGLVNSSLFVEDCKLPLGQSLCAL
PDTPGEMRLASIAFNHPIQVDQLNSSYFKLSIPTNFSFGVTQEYIQTTIQ
KVTVDCKQYVCNGFQKCEQLLREYGQFCSKINQALHGANLRQDDSVRNLF
ASVKSSQSSPIIPGFGGDFNLTLLEPVARSAIEDLLFDKVTIADPGYMQG
YDDCMQQGPASARDLICAQYVAGYKVLPPLMDVNMEAAYTSSLLGSIAGV
GWTAGLSSFAAIPFAQSIFYRLNGVGITQQVLSENQKLIANKFNQALGAM
QTGFTTTNEAFQKVQDAVNNNAQALSKLASELSNTFGAISASIGDIIQRL
DPPEQDAQIDRLINGRLTTLNAFVAQQLVRSESAALSAQLAKDKVNECVK
AQSKRSGFCGQGTHIVSFVVNAPNGLYFMHVGYYPSNHIEVVSAYGLCDA
ANPTNCIAPVNGYFIKTEWSYTGSSFYAPEPITSLNTKYVAPQVTYQNIS
TNLPPPLLG
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 chain6q04 Chain B Residue 1445 [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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PDB6q04 Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Q36 F39 A92 F101 I132 S133 R307
Binding residue
(residue number reindexed from 1)		Q19 F22 A75 F84 I115 S116 R290
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
Biological Process
GO:0019062 virion attachment to host cell
GO:0019064 fusion of virus membrane with host plasma membrane
GO:0019065 receptor-mediated endocytosis of virus by host cell
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:0061025 membrane fusion
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:6q04, PDBe:6q04, PDBj:6q04
PDBsum6q04
PubMed31792450
UniProtK0BRG7

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