Structure of PDB 4r09 Chain D Binding Site BS03

Receptor Information
>4r09 Chain D (length=746) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSYPCDEKKQVIAECSNRRLQEVPQTVGKYVTELDLSDNFITHITNESFQ
GLQNLTKINLNHNPNNGLNITDGAFLNLKNLRELLLEDNQLPQIPSGLPE
SLTELSLIQNNIYNITKEGISRLINLKNLYLAWNCYFNKVCEKTNIEDGV
FETLTNLELLSLSFNSLSHVPPKLPSSLRKLFLSNTQIKYISEEDFKGLI
NLTLLDLSGNCPRCFNAPFPCVPCDGGASINIDRFAFQNLTQLRYLNLSS
TSLRKINAAWFKNMPHLKVLDLEFNYLVGEIASGAFLTMLPRLEILDLSF
NYIKGSYPQHINISRNFSKLLSLRALHLRGYVFQELREDDFQPLMQLPNL
STINLGINFIKQIDFKLFQNFSNLEIIYLSENRISPLDFEFDPHSNFYHF
TRPLIKPQCAAYGKALDLSLNSIFFIGPNQFENLPDIACLNLSANSNAQV
LSGTEFSAIPHVKYLDLTNNRLDFDNASALTELSDLEVLDLSYNSHYFRI
AGVTHHLEFIQNFTNLKVLNLSHNNIYTLTDKYNLESKSLVELVFSGNRL
DILWNDDDNRYISIFKGLKNLTRLDLSLNRLKHIPNEAFLNLPASLTELH
INDNMLKFFNWTLLQQFPRLELLDLRGNKLLFLTDSLSDFTSSLRTLLLS
HNRISHLPSGFLSEVSSLKHLDLSSNLLKTINKSALETKTTTKLSMLELH
GNPFECTCDIGDFRRWMDEHLNVKIPRLVDVICASPGDQRGKSIVS
Ligand information
Ligand ID06S
InChIInChI=1S/C19H26N7O16P3S3/c20-18-23-14-9(15(30)24-18)21-5-26(14)17-10(28)12(41-44(34,35)47)7(40-17)4-38-45(36,48)42-13-6(3-37-43(32,33)46)39-16(11(13)29)25-2-1-8(27)22-19(25)31/h1-2,5-7,10-13,16-17,28-29H,3-4H2,(H,36,48)(H,22,27,31)(H2,32,33,46)(H2,34,35,47)(H3,20,23,24,30)/t6-,7-,10-,11-,12-,13-,16-,17-,45+/m1/s1
InChIKeyPRHQISJBVGJFKN-VXGQQCRQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=NC(=O)c2ncn([CH]3O[CH](CO[P](S)(=O)O[CH]4[CH](O)[CH](O[CH]4CO[P](O)(S)=O)N5C=CC(=O)NC5=O)[CH](O[P](O)(S)=O)[CH]3O)c2N1
CACTVS 3.385NC1=NC(=O)c2ncn([C@@H]3O[C@H](CO[P@@](S)(=O)O[C@H]4[C@@H](O)[C@@H](O[C@@H]4CO[P](O)(S)=O)N5C=CC(=O)NC5=O)[C@@H](O[P](O)(S)=O)[C@H]3O)c2N1
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(OC4C(OC(C4O)N5C=CC(=O)NC5=O)COP(=O)(O)S)S)OP(=O)(O)S)O)NC(=NC2=O)N
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O[C@@H]4[C@H](O[C@H]([C@@H]4O)N5C=CC(=O)NC5=O)COP(=O)(O)S)S)OP(=O)(O)S)O)NC(=NC2=O)N
ACDLabs 12.01O=P(O)(S)OC1C(O)C(OC1COP(=O)(S)OC3C(OC(N2C(=O)NC(=O)C=C2)C3O)COP(=O)(O)S)n4c5NC(=NC(=O)c5nc4)N
FormulaC19 H26 N7 O16 P3 S3
NameO-[(2R,3S,4R,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-2-({[(S)-({(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-[(thiophosphonooxy)methyl]tetrahydrofuran-3-yl}oxy)(sulfanyl)phosphoryl]oxy}methyl)-4-hydroxytetrahydrofuran-3-yl] dihydrogen (S)-phosphorothioate
ChEMBL
DrugBank
ZINC
PDB chain4r09 Chain D Residue 903 [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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PDB4r09 Toll-like receptor 8 senses degradation products of single-stranded RNA.
Resolution2.62 Å
Binding residue
(original residue number in PDB)
Y291 I341 D343 H373 R375 H469 T471 L474
Binding residue
(residue number reindexed from 1)
Y245 I295 D297 H327 R329 H399 T401 L404
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004888 transmembrane signaling receptor activity
Biological Process
GO:0002224 toll-like receptor signaling pathway
GO:0006955 immune response
Cellular Component
GO:0016020 membrane

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:4r09, PDBe:4r09, PDBj:4r09
PDBsum4r09
PubMed25599397
UniProtQ9NR97|TLR8_HUMAN Toll-like receptor 8 (Gene Name=TLR8)

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