Structure of PDB 4r07 Chain D Binding Site BS02

Receptor Information
>4r07 Chain D (length=735) 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
ISHLPSGFLSEVSSLKHLDLSSNLLKTINKLSMLELHGNPFECTCDIGDF
RRWMDEHLNVKIPRLVDVICASPGDQRGKSIVSLE
Ligand information
Ligand IDURI
InChIInChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1
InChIKeyDRTQHJPVMGBUCF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)CO
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)O
CACTVS 3.341OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O
FormulaC9 H12 N2 O6
NameURIDINE
ChEMBLCHEMBL100259
DrugBankDB02745
ZINCZINC000002583633
PDB chain4r07 Chain D Residue 901 [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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PDB4r07 Toll-like receptor 8 senses degradation products of single-stranded RNA
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Y348 K350 G351 Y353 V378 F405 R429
Binding residue
(residue number reindexed from 1)		Y300 K302 G303 Y305 V330 F357 R381
Annotation score4
Binding affinityMOAD: Kd=55uM
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
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Biological Process
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Cellular Component
External links
PDB RCSB:4r07, PDBe:4r07, PDBj:4r07
PDBsum4r07
PubMed25599397
UniProtQ9NR97|TLR8_HUMAN Toll-like receptor 8 (Gene Name=TLR8)

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