Structure of PDB 1lpd Chain A Binding Site BS01

Receptor Information
>1lpd Chain A (length=254) Species: 3570 (Dianthus caryophyllus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATAYTLNLANPSASQYSSFLDQIRNNVRDTSLIYGGTDVEVIGAPSTTDK
FLRLNFQGPRGTVSLGLRRENLYVVAYLAMDNANVNRAYYFKNQITSAEL
TALFPEVVVANQKQLEYGEDYQAIEKNAKITTGDQSRKELGLGINLLITM
IDGVNKKVRVVKDEARFLLIAIQMTAEAARFRYIQNLVTKNFPNKFDSEN
KVIQFQVSWSKISTAIFGDCKNGVFNKDYDFGFGKVRQAKDLQMGLLKYL
GRPK
Ligand information
Ligand IDADE
InChIInChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)
InChIKeyGFFGJBXGBJISGV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2[nH]cnc12
OpenEye OEToolkits 1.5.0c1[nH]c2c(n1)c(ncn2)N
ACDLabs 10.04n1c(c2ncnc2nc1)N
FormulaC5 H5 N5
NameADENINE
ChEMBLCHEMBL226345
DrugBankDB00173
ZINCZINC000000000882
PDB chain1lpd Chain A Residue 901 [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]
PDB1lpd High resolution X-ray structure and potent anti-HIV activity of recombinant dianthin antiviral protein.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		Y73 V74 E119 I172 R180
Binding residue
(residue number reindexed from 1)		Y73 V74 E119 I172 R180
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) E177 R180
Catalytic site (residue number reindexed from 1) E177 R180
Enzyme Commision number 3.2.2.22: rRNA N-glycosylase.
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0030598 rRNA N-glycosylase activity
GO:0090729 toxin activity
Biological Process
GO:0006952 defense response
GO:0017148 negative regulation of translation
GO:0035821 modulation of process of another organism
GO:0050688 regulation of defense response to virus

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1lpd, PDBe:1lpd, PDBj:1lpd
PDBsum1lpd
PubMed15553110
UniProtP24476|RIP0_DIACA Ribosome-inactivating protein dianthin-30

[Back to BioLiP]