Structure of PDB 1nli Chain A Binding Site BS01

Receptor Information
>1nli Chain A (length=248) Species: 3677 (Trichosanthes kirilowii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYAL
IHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDA
MRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAAS
ALMVLIQSTSAAARYKFIEQQIGKRVDKTFLPSLAIISLANSWSALSKQI
QIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA
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 chain1nli Chain A Residue 248 [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]
PDB1nli Structural basis for the interaction of [E160A-E189A]-trichosanthin with adenine.
Resolution1.93 Å
Binding residue
(original residue number in PDB)		Y70 I71 G109 Y111 I155 S159 R163
Binding residue
(residue number reindexed from 1)		Y71 I72 G110 Y112 I156 S160 R164
Annotation score4
Binding affinityMOAD: Kd=260uM
PDBbind-CN: -logKd/Ki=3.59,Kd=260uM
Enzymatic activity
Catalytic site (original residue number in PDB) I71 A160 R163
Catalytic site (residue number reindexed from 1) I72 A161 R164
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:1nli, PDBe:1nli, PDBj:1nli
PDBsum1nli
PubMed12676436
UniProtP09989|RIPT_TRIKI Ribosome-inactivating protein alpha-trichosanthin

[Back to BioLiP]