Structure of PDB 6hkv Chain D Binding Site BS01

Receptor Information
>6hkv Chain D (length=263) Species: 862909 (Trichodysplasia spinulosa-associated polyomavirus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IEVLNLVTGPDSITTIELYLNTRMGQNDESKDNYGYSEKVTVANSSDQDK
PTSGEIPTYSTARINLPMLTLTMWEAVSVKTEVVGVSSLVNVHMATKRMY
DDKGIGFPVEGMNFHMFAVGGEPLELQFLTGNYRTDYSANDKLVVPPIKH
QSTQGLNPHYKQKLTKDGAFPVECWCPDPSKNENTRYYGSYTGGQSTPPV
LQFTNTVTTVLLDENGVGPLCKGDGLYVSCCDIVGFLVGKDGDMQYRGLP
RYFNILLRKRTVR
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 D 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)		T73 V74 A75 K82 T84
Binding residue
(residue number reindexed from 1)		T41 V42 A43 K50 T52
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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