Structure of PDB 3rt4 Chain D Binding Site BS01

Receptor Information
>3rt4 Chain D (length=171) Species: 9838 (Camelus dromedarius) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EDPPACGSIVPRREWRALASECRERLTRPVRYVVVSHTAGSHCDTPASCA
QQAQNVQSYHVRNLGWCDVGYNFLIGEDGLVYEGRGWNIKGAHAGPTWNP
ISIGISFMGNYMNRVPPPRALRAAQNLLACGVALGALRSNYEVKGHRDVQ
PTLSPGDRLYEIIQTWSHYRA
Ligand information
Ligand IDLP5
InChIInChI=1S/C34H66NO12P/c1-3-5-7-9-11-13-15-17-19-21-26(37)23-29(39)35-31-33(32(41)28(25-36)45-34(31)47-48(42,43)44)46-30(40)24-27(38)22-20-18-16-14-12-10-8-6-4-2/h26-28,31-34,36-38,41H,3-25H2,1-2H3,(H,35,39)(H2,42,43,44)/t26-,27-,28-,31-,32-,33-,34-/m1/s1
InChIKeyHEHQDWUWJVPREQ-XQJZMFRCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCCCCCCCC[C@@H](O)CC(=O)N[C@H]1[C@H](O[C@H](CO)[C@@H](O)[C@@H]1OC(=O)C[C@H](O)CCCCCCCCCCC)O[P](O)(O)=O
OpenEye OEToolkits 1.5.0CCCCCCCCCCC[C@H](CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1OP(=O)(O)O)CO)O)OC(=O)C[C@@H](CCCCCCCCCCC)O)O
ACDLabs 10.04O=P(OC1OC(C(O)C(OC(=O)CC(O)CCCCCCCCCCC)C1NC(=O)CC(O)CCCCCCCCCCC)CO)(O)O
OpenEye OEToolkits 1.5.0CCCCCCCCCCCC(CC(=O)NC1C(C(C(OC1OP(=O)(O)O)CO)O)OC(=O)CC(CCCCCCCCCCC)O)O
CACTVS 3.341CCCCCCCCCCC[CH](O)CC(=O)N[CH]1[CH](O[CH](CO)[CH](O)[CH]1OC(=O)C[CH](O)CCCCCCCCCCC)O[P](O)(O)=O
FormulaC34 H66 N O12 P
Name(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE
ChEMBL
DrugBank
ZINCZINC000058650130
PDB chain3rt4 Chain C Residue 501 [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]
PDB3rt4 Structural Basis of Recognition of Pathogen-associated Molecular Patterns and Inhibition of Proinflammatory Cytokines by Camel Peptidoglycan Recognition Protein.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G95 P96 T97 W98 K144 D148 V149 Q150 P151
Binding residue
(residue number reindexed from 1)		G95 P96 T97 W98 K144 D148 V149 Q150 P151
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.80,Kd=1.6nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y71 T152
Catalytic site (residue number reindexed from 1) Y71 T152
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0008745 N-acetylmuramoyl-L-alanine amidase activity
GO:0016019 peptidoglycan immune receptor activity
GO:0042834 peptidoglycan binding
Biological Process
GO:0001818 negative regulation of cytokine production
GO:0009253 peptidoglycan catabolic process
GO:0016045 detection of bacterium
GO:0042742 defense response to bacterium
GO:0045087 innate immune response
GO:0050830 defense response to Gram-positive bacterium
Cellular Component
GO:0005576 extracellular region

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3rt4, PDBe:3rt4, PDBj:3rt4
PDBsum3rt4
PubMed21454594
UniProtQ9GK12|PGRP1_CAMDR Peptidoglycan recognition protein 1 (Gene Name=PGLYRP1)

[Back to BioLiP]