Structure of PDB 4r08 Chain A Binding Site BS02

Receptor Information
>4r08 Chain A (length=743) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSYPCDEKKQVIAECSNRRLQEVPQTVGKYVTELDLSDNFITHITNESFQ
GLQNLTKINLNHNPNVNGLNITDGAFLNLKNLRELLLEDNQLPQIPSGLP
ESLTELSLIQNNIYNITKEGISRLINLKNLYLAWNCYFNKVCEKTNIEDG
VFETLTNLELLSLSFNSLSHVPPKLPSSLRKLFLSNTQIKYISEEDFKGL
INLTLLDLSGNCPRCFNAPFPCVPCDGGASINIDRFAFQNLTQLRYLNLS
STSLRKINAAWFKNMPHLKVLDLEFNYLVGEIASGAFLTMLPRLEILDLS
FNYIKGSYPQHINISRNFSKLLSLRALHLRGYVFQELREDDFQPLMQLPN
LSTINLGINFIKQIDFKLFQNFSNLEIIYLSENRISPDFEFDPHSNFYHF
TRPLIKPQCAAYGKALDLSLNSIFFIGPNQFENLPDIACLNLSANSNAQV
LSGTEFSAIPHVKYLDLTNNRLDFDNASALTELSDLEVLDLSYNSHYFRI
AGVTHHLEFIQNFTNLKVLNLSHNNIYTLTDKYNLESKSLVELVFSGNRL
DILWNDDDNRYISIFKGLKNLTRLDLSLNRLKHIPNEAFLNLPASLTELH
INDNMLKFFNWTLLQQFPRLELLDLRGNKLLFLTDSLSDFTSSLRTLLLS
HNRISHLPSGFLSEVSSLKHLDLSSNLLKTINKSALEKLSMLELHGNPFE
CTCDIGDFRRWMDEHLNVKIPRLVDVICASPGDQRGKSIVSLE
Ligand information
Ligand IDUCG
InChIInChI=1S/C19H24N7O18P3/c20-18-23-14-9(15(29)24-18)21-5-26(14)17-13-12(43-47(36,37)44-13)7(41-17)4-39-46(34,35)42-11-6(3-38-45(31,32)33)40-16(10(11)28)25-2-1-8(27)22-19(25)30/h1-2,5-7,10-13,16-17,28H,3-4H2,(H,34,35)(H,36,37)(H,22,27,30)(H2,31,32,33)(H3,20,23,24,29)/t6-,7-,10-,11-,12-,13-,16-,17-/m1/s1
InChIKeyUIVVUPHFWRPLKC-VMIOUTBZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C4C(C(O3)COP(=O)(O)OC5C(OC(C5O)N6C=CC(=O)NC6=O)COP(=O)(O)O)OP(=O)(O4)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OCC6OC(N1C=CC(=O)NC1=O)C(O)C6OP(=O)(O)OCC4OC(n2c3N=C(N)NC(=O)c3nc2)C5OP(=O)(O)OC45
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@H]4[C@@H]([C@H](O3)COP(=O)(O)O[C@@H]5[C@H](O[C@H]([C@@H]5O)N6C=CC(=O)NC6=O)COP(=O)(O)O)OP(=O)(O4)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[CH]4[CH](O)[CH](O[CH]4CO[P](O)(O)=O)N5C=CC(=O)NC5=O)[CH]6O[P](O)(=O)O[CH]36
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[C@H]4[C@@H](O)[C@@H](O[C@@H]4CO[P](O)(O)=O)N5C=CC(=O)NC5=O)[C@H]6O[P](O)(=O)O[C@@H]36
FormulaC19 H24 N7 O18 P3
Name3'-O-[(R)-{[(2R,3aR,4R,6R,6aR)-6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]uridine 5'-(dihydrogen phosphate)
ChEMBL
DrugBank
ZINCZINC000222071831
PDB chain4r08 Chain A Residue 915 [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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PDB4r08 Toll-like receptor 8 senses degradation products of single-stranded RNA.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
I341 D343 H373 R375 H469 F470 T471 R472 P473 L474
Binding residue
(residue number reindexed from 1)
I296 D298 H328 R330 H399 F400 T401 R402 P403 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:4r08, PDBe:4r08, PDBj:4r08
PDBsum4r08
PubMed25599397
UniProtQ9NR97|TLR8_HUMAN Toll-like receptor 8 (Gene Name=TLR8)

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