Structure of PDB 3ula Chain D Binding Site BS01

Receptor Information
>3ula Chain D (length=140) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPR
RDLKQLYFNLYITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTIS
FSFKGIKFSKGKYKCVVEAISGSPEEMLFCLEFVILHQPN
Ligand information
Ligand IDE55
InChIInChI=1S/C66H126N2O19P2/c1-7-11-15-19-22-25-26-27-28-29-30-32-34-38-42-46-57(70)67-60-64(82-49-47-54(80-6)45-41-36-18-14-10-4)62(86-88(73,74)75)56(51-79-5)85-65(60)83-52-55-61(72)63(81-48-43-39-35-24-21-17-13-9-3)59(66(84-55)87-89(76,77)78)68-58(71)50-53(69)44-40-37-33-31-23-20-16-12-8-2/h25-26,54-56,59-66,72H,7-24,27-52H2,1-6H3,(H,67,70)(H,68,71)(H2,73,74,75)(H2,76,77,78)/b26-25-/t54-,55-,56-,59-,60-,61-,62-,63-,64-,65-,66-/m1/s1
InChIKeyBPSMYQFMCXXNPC-MFCPCZTFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCCCCCCCCC(=O)CC(=O)NC1C(C(C(OC1OP(=O)(O)O)COC2C(C(C(C(O2)COC)OP(=O)(O)O)OCCC(CCCCCCC)OC)NC(=O)CCCCCCCCCC=CCCCCCC)O)OCCCCCCCCCC
CACTVS 3.341CCCCCCCCCCCC(=O)CC(=O)N[C@H]1[C@H](O[C@H](CO[C@@H]2O[C@H](COC)[C@@H](O[P](O)(O)=O)[C@H](OCC[C@@H](CCCCCCC)OC)[C@H]2NC(=O)CCCCCCCCC\C=C/CCCCCC)[C@@H](O)[C@@H]1OCCCCCCCCCC)O[P](O)(O)=O
ACDLabs 10.04O=P(OC1OC(C(O)C(OCCCCCCCCCC)C1NC(=O)CC(=O)CCCCCCCCCCC)COC2OC(COC)C(OP(=O)(O)O)C(OCCC(OC)CCCCCCC)C2NC(=O)CCCCCCCCC\C=C/CCCCCC)(O)O
OpenEye OEToolkits 1.5.0CCCCCCCCCCCC(=O)CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1OP(=O)(O)O)CO[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)COC)OP(=O)(O)O)OCC[C@@H](CCCCCCC)OC)NC(=O)CCCCCCCCC\C=C/CCCCCC)O)OCCCCCCCCCC
CACTVS 3.341CCCCCCCCCCCC(=O)CC(=O)N[CH]1[CH](O[CH](CO[CH]2O[CH](COC)[CH](O[P](O)(O)=O)[CH](OCC[CH](CCCCCCC)OC)[CH]2NC(=O)CCCCCCCCCC=CCCCCCC)[CH](O)[CH]1OCCCCCCCCCC)O[P](O)(O)=O
FormulaC66 H126 N2 O19 P2
Name3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE;
E5564;
ERITORAN
ChEMBLCHEMBL501259
DrugBankDB04933
ZINC
PDB chain3ula Chain A Residue 1206 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ula Structure-Based Rational Design of a Toll-like Receptor 4 (TLR4) Decoy Receptor with High Binding Affinity for a Target Protein.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		I52 F76 I117 F119 S120 F121 F151
Binding residue
(residue number reindexed from 1)		I34 F58 I99 F101 S102 F103 F133
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001530 lipopolysaccharide binding
GO:0001875 lipopolysaccharide immune receptor activity
GO:0005515 protein binding
GO:0015026 coreceptor activity
GO:0035662 Toll-like receptor 4 binding
Biological Process
GO:0002224 toll-like receptor signaling pathway
GO:0006954 inflammatory response
GO:0006968 cellular defense response
GO:0007166 cell surface receptor signaling pathway
GO:0031663 lipopolysaccharide-mediated signaling pathway
GO:0031666 positive regulation of lipopolysaccharide-mediated signaling pathway
GO:0032496 response to lipopolysaccharide
GO:0032497 detection of lipopolysaccharide
GO:0032760 positive regulation of tumor necrosis factor production
GO:0034142 toll-like receptor 4 signaling pathway
GO:0045087 innate immune response
GO:0071222 cellular response to lipopolysaccharide
Cellular Component
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0010008 endosome membrane
GO:0043235 receptor complex
GO:0046696 lipopolysaccharide receptor complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3ula, PDBe:3ula, PDBj:3ula
PDBsum3ula
PubMed22363519
UniProtQ9Y6Y9|LY96_HUMAN Lymphocyte antigen 96 (Gene Name=LY96)

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