Structure of PDB 4r07 Chain C Binding Site BS02

Receptor Information
>4r07 Chain C (length=738) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSYPCDEKVIAECSNRRLQEVPQTVGKYVTELDLSDNFITHITNESFQGL
QNLTKINLNHNPNVGLNITDGAFLNLKNLRELLLEDNQLPQIPSGLPESL
TELSLIQNNIYNITKEGISRLINLKNLYLAWNCYFNKVCEKTNIEDGVFE
TLTNLELLSLSFNSLSHVPPKLPSSLRKLFLSNTQIKYISEEDFKGLINL
TLLDLSGNCPRCFNAPFPCVPCDGGASINIDRFAFQNLTQLRYLNLSSTS
LRKINAAWFKNMPHLKVLDLEFNYLVGEIASGAFLTMLPRLEILDLSFNY
IKGSYPQHINISRNFSKLLSLRALHLRGYVFQELREDDFQPLMQLPNLST
INLGINFIKQIDFKLFQNFSNLEIIYLSENRISPDFEFDPHSNFYHFTRP
LIKPQCAAYGKALDLSLNSIFFIGPNQFENLPDIACLNLSANSNAQVLSG
TEFSAIPHVKYLDLTNNRLDFDNASALTELSDLEVLDLSYNSHYFRIAGV
THHLEFIQNFTNLKVLNLSHNNIYTLTDKYNLESKSLVELVFSGNRLDIL
WNDDDNRYISIFKGLKNLTRLDLSLNRLKHIPNEAFLNLPASLTELHIND
NMLKFFNWTLLQQFPRLELLDLRGNKLLFLTDSLSDFTSSLRTLLLSHNR
ISHLPSGFLSEVSSLKHLDLSSNLLKTINTTTKLSMLELHGNPFECTCDI
GDFRRWMDEHLNVKIPRLVDVICASPGDQRGKSIVSLE
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 chain4r07 Chain C Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4r07 Toll-like receptor 8 senses degradation products of single-stranded RNA
Resolution2.0 Å
Binding residue
(original residue number in PDB)
K314 V315 E340 I341 D343 R370 H373 R375 H469 T471 R472 P473 L474
Binding residue
(residue number reindexed from 1)
K266 V267 E292 I293 D295 R322 H325 R327 H396 T398 R399 P400 L401
Annotation score1
Binding affinityMOAD: Kd=4.8uM
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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:4r07, PDBe:4r07, PDBj:4r07
PDBsum4r07
PubMed25599397
UniProtQ9NR97|TLR8_HUMAN Toll-like receptor 8 (Gene Name=TLR8)

[Back to BioLiP]