Structure of PDB 3hit Chain A Binding Site BS01

Receptor Information
>3hit Chain A (length=257) Species: 3572 (Saponaria officinalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPK
FLRVNLKASTGTVSLAVQRSNLYVAAYLAKNNNKQFRAYYFKGFQITTNQ
LNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTK
VNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPD
RVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEI
GIFLNVD
Ligand information
Ligand IDDYN
InChIInChI=1S/C30H47N10O17P3/c1-50-25-24(57-59(46,47)52-7-3-2-5-41)20(55-29(25)40-16-36-23-27(40)37-30(32)38-28(23)43)14-54-60(48,49)56-19-12-39(10-17-9-33-22-21(17)34-15-35-26(22)31)11-18(19)13-53-58(44,45)51-8-4-6-42/h9,15-16,18-20,24-25,29,33,41-42H,2-8,10-14H2,1H3,(H,44,45)(H,46,47)(H,48,49)(H2,31,34,35)(H3,32,37,38,43)/t18-,19+,20-,24-,25-,29-/m1/s1
InChIKeyQYBAOMLZOZKJGY-BLRDUOQJSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CO[CH]1[CH](O[P](O)(=O)OCCCCO)[CH](CO[P](O)(=O)O[CH]2CN(C[CH]2CO[P](O)(=O)OCCCO)Cc3c[nH]c4c(N)ncnc34)O[CH]1n5cnc6C(=O)NC(=Nc56)N
OpenEye OEToolkits 1.7.0COC1C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)OC4CN(CC4COP(=O)(O)OCCCO)Cc5c[nH]c6c5ncnc6N)OP(=O)(O)OCCCCO
CACTVS 3.352CO[C@@H]1[C@H](O[P](O)(=O)OCCCCO)[C@@H](CO[P](O)(=O)O[C@H]2CN(C[C@@H]2CO[P](O)(=O)OCCCO)Cc3c[nH]c4c(N)ncnc34)O[C@H]1n5cnc6C(=O)NC(=Nc56)N
OpenEye OEToolkits 1.7.0CO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)CO[P@](=O)(O)O[C@H]4C[N@@](C[C@@H]4CO[P@@](=O)(O)OCCCO)Cc5c[nH]c6c5ncnc6N)O[P@](=O)(O)OCCCCO
ACDLabs 11.02O=P(OCCCO)(O)OCC6CN(Cc2c1ncnc(N)c1nc2)CC6OP(=O)(O)OCC5OC(n4cnc3c4N=C(N)NC3=O)C(OC)C5OP(=O)(OCCCCO)O
FormulaC30 H47 N10 O17 P3
Name
ChEMBL
DrugBank
ZINCZINC000198010166
PDB chain3hit Chain A Residue 260 [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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PDB3hit Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.
Resolution2.29 Å
Binding residue
(original residue number in PDB)		Y73 V74 E121 Y123 V169 E174 R177 E206 N207 W209 G210 R214 Y233 L254
Binding residue
(residue number reindexed from 1)		Y73 V74 E121 Y123 V169 E174 R177 E206 N207 W209 G210 R214 Y233 L254
Annotation score1
Binding affinityMOAD: Ki=6.4nM
PDBbind-CN: -logKd/Ki=8.19,Ki=6.4nM
Enzymatic activity
Catalytic site (original residue number in PDB) V74 E174 R177
Catalytic site (residue number reindexed from 1) V74 E174 R177
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3hit, PDBe:3hit, PDBj:3hit
PDBsum3hit
PubMed19920175
UniProtQ2QEH4

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