Structure of PDB 6hkv Chain C Binding Site BS02

Receptor Information
>6hkv Chain C (length=272) Species: 862909 (Trichodysplasia spinulosa-associated polyomavirus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NIEVLNLVTGPDSITTIELYLNTRMGQNDESKDNYGYSEKVTVANSSDQD
KPTSGEIPTYSTARINLPMLNEDLTSNTLTMWEAVSVKTEVVGVSSLVNV
HMATKRMYDDKGIGFPVEGMNFHMFAVGGEPLELQFLTGNYRTDYSANDK
LVVPPIKHQSTQGLNPHYKQKLTKDGAFPVECWCPDPSKNENTRYYGSYT
GGQSTPPVLQFTNTVTTVLLDENGVGPLCKGDGLYVSCCDIVGFLVGKDG
DMQYRGLPRYFNILLRKRTVRN
Ligand information
Ligand IDGXB
InChIInChI=1S/C92H139N19O39/c1-58(114)94-22-32-108(87(133)63-8-4-61(5-9-63)50-110-52-65(104-106-110)56-145-91(89(135)136)48-67(117)83(147-59(2)115)85(149-91)81(131)69(119)54-112)33-24-96-73(123)14-16-75(125)98-26-36-139-42-44-141-38-28-100-77(127)18-20-79(129)102-30-40-143-46-47-144-41-31-103-80(130)21-19-78(128)101-29-39-142-45-43-140-37-27-99-76(126)17-15-74(124)97-25-35-109(34-23-95-72(122)13-12-71(93)121)88(134)64-10-6-62(7-11-64)51-111-53-66(105-107-111)57-146-92(90(137)138)49-68(118)84(148-60(3)116)86(150-92)82(132)70(120)55-113/h4-11,52-53,67-70,81-86,112-113,117-120,131-132H,12-51,54-57H2,1-3H3,(H2,93,121)(H,94,114)(H,95,122)(H,96,123)(H,97,124)(H,98,125)(H,99,126)(H,100,127)(H,101,128)(H,102,129)(H,103,130)(H,135,136)(H,137,138)/t67?,68-,69?,70+,81?,82+,83?,84+,85?,86-,91?,92+/m0/s1
InChIKeyNBOMXQZYLQVMQG-PGDFXJOBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)NCCN(CCNC(=O)CCC(=O)NCCOCCOCCNC(=O)CCC(=O)NCCOCCOCCNC(=O)CCC(=O)NCCOCCOCCNC(=O)CCC(=O)NCCN(CCNC(=O)CCC(N)=O)C(=O)c1ccc(Cn2cc(CO[C@@]3(C[C@H](O)[C@@H](OC(C)=O)[C@@H](O3)[C@H](O)[C@H](O)CO)C(O)=O)nn2)cc1)C(=O)c4ccc(Cn5cc(COC6(CC(O)C(OC(C)=O)C(O6)C(O)C(O)CO)C(O)=O)nn5)cc4
OpenEye OEToolkits 2.0.6CC(=O)NCCN(CCNC(=O)CCC(=O)NCCOCCOCCNC(=O)CCC(=O)NCCOCCOCCNC(=O)CCC(=O)NCCOCCOCCNC(=O)CCC(=O)NCCN(CCNC(=O)CCC(=O)N)C(=O)c1ccc(cc1)Cn2cc(nn2)COC3(CC(C(C(O3)C(C(CO)O)O)OC(=O)C)O)C(=O)O)C(=O)c4ccc(cc4)Cn5cc(nn5)COC6(CC(C(C(O6)C(C(CO)O)O)OC(=O)C)O)C(=O)O
OpenEye OEToolkits 2.0.6CC(=O)NCCN(CCNC(=O)CCC(=O)NCCOCCOCCNC(=O)CCC(=O)NCCOCCOCCNC(=O)CCC(=O)NCCOCCOCCNC(=O)CCC(=O)NCCN(CCNC(=O)CCC(=O)N)C(=O)c1ccc(cc1)Cn2cc(nn2)CO[C@@]3(C[C@@H]([C@H]([C@@H](O3)[C@@H]([C@@H](CO)O)O)OC(=O)C)O)C(=O)O)C(=O)c4ccc(cc4)Cn5cc(nn5)COC6(CC(C(C(O6)C(C(CO)O)O)OC(=O)C)O)C(=O)O
CACTVS 3.385CC(=O)NCCN(CCNC(=O)CCC(=O)NCCOCCOCCNC(=O)CCC(=O)NCCOCCOCCNC(=O)CCC(=O)NCCOCCOCCNC(=O)CCC(=O)NCCN(CCNC(=O)CCC(N)=O)C(=O)c1ccc(Cn2cc(CO[C]3(C[CH](O)[CH](OC(C)=O)[CH](O3)[CH](O)[CH](O)CO)C(O)=O)nn2)cc1)C(=O)c4ccc(Cn5cc(COC6(CC(O)C(OC(C)=O)C(O6)C(O)C(O)CO)C(O)=O)nn5)cc4
FormulaC92 H139 N19 O39
NameSialylated precision glycomacromolecule
ChEMBL
DrugBank
ZINC
PDB chain6hkv Chain I Residue 401 [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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PDB6hkv Divalent Sialylated Precision Glycooligomers Binding to Polyomaviruses and the Effect of Different Linkers.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		L36 R299
Binding residue
(residue number reindexed from 1)		L5 R268
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005198 structural molecule activity
Cellular Component
GO:0019028 viral capsid

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:6hkv, PDBe:6hkv, PDBj:6hkv
PDBsum6hkv
PubMed30884172
UniProtE2ESL7

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