Structure of PDB 3hiv Chain B Binding Site BS01

Receptor Information
>3hiv Chain B (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 IDTXN
InChIInChI=1S/C37H52N15O20P3/c1-63-27-25(19(10-54)68-34(27)51-14-44-23-30(51)46-36(39)48-32(23)55)71-75(61,62)66-11-17-8-50(7-16-6-41-22-21(16)42-13-43-29(22)38)9-18(17)70-74(59,60)67-12-20-26(72-73(57,58)65-5-3-4-53)28(64-2)35(69-20)52-15-45-24-31(52)47-37(40)49-33(24)56/h6,13,15,17-20,25-28,34-35,41,53-54H,3-5,7-12,14H2,1-2H3,(H,57,58)(H,59,60)(H,61,62)(H2,38,42,43)(H2,39,48,55)(H3,40,47,49,56)/t17-,18+,19-,20-,25-,26-,27-,28-,34-,35-/m1/s1
InChIKeyXYVXLTGAFUOPLT-UTNLYJRASA-N
SMILES
SoftwareSMILES
CACTVS 3.352CO[C@@H]1[C@H](O[P](O)(=O)OC[C@H]2CN(C[C@@H]2O[P](O)(=O)OC[C@H]3O[C@H]([C@H](OC)[C@@H]3O[P](O)(=O)OCCCO)n4cnc5C(=O)N=C(N)Nc45)Cc6c[nH]c7c(N)ncnc67)[C@@H](CO)O[C@H]1N8CN=C9C(=O)N=C(N)N=C89
OpenEye OEToolkits 1.7.0COC1C(C(OC1n2cnc3c2NC(=NC3=O)N)COP(=O)(O)OC4CN(CC4COP(=O)(O)OC5C(OC(C5OC)N6CN=C7C6=NC(=NC7=O)N)CO)Cc8c[nH]c9c8ncnc9N)OP(=O)(O)OCCCO
OpenEye OEToolkits 1.7.0CO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2NC(=NC3=O)N)CO[P@](=O)(O)O[C@H]4CN(C[C@@H]4CO[P@](=O)(O)O[C@@H]5[C@H](O[C@H]([C@@H]5OC)N6CN=C7C6=NC(=NC7=O)N)CO)Cc8c[nH]c9c8ncnc9N)O[P@@](=O)(O)OCCCO
CACTVS 3.352CO[CH]1[CH](O[P](O)(=O)OC[CH]2CN(C[CH]2O[P](O)(=O)OC[CH]3O[CH]([CH](OC)[CH]3O[P](O)(=O)OCCCO)n4cnc5C(=O)N=C(N)Nc45)Cc6c[nH]c7c(N)ncnc67)[CH](CO)O[CH]1N8CN=C9C(=O)N=C(N)N=C89
ACDLabs 11.02O=C9N=C(N=C1C9=NCN1C8OC(CO)C(OP(=O)(O)OCC7CN(Cc3c2ncnc(N)c2nc3)CC7OP(=O)(O)OCC6OC(n4cnc5c4NC(=NC5=O)N)C(OC)C6OP(=O)(OCCCO)O)C8OC)N
FormulaC37 H52 N15 O20 P3
Name(2R,3R,4R,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-2-({[(S)-({(3R,4R)-4-({[(S)-{[(2R,3R,4R,5R)-5-(2-amino-6-oxo-6,8-dihydro-9H-purin-9-yl)-2-(hydroxymethyl)-4-methoxytetrahydrofuran-3-yl]oxy}(hydroxy)phosphoryl]oxy}methyl)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]pyrrolidin-3-yl}oxy)(hydroxy)phosphoryl]oxy}methyl)-4-methoxytetrahydrofuran-3-yl 3-hydroxypropyl hydrogen (S)-phosphate
ChEMBL
DrugBank
ZINC
PDB chain3hiv Chain B 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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PDB3hiv Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.
Resolution2.14 Å
Binding residue
(original residue number in PDB)
N71 Y73 V74 E121 S122 Y123 E174 R177 E206 W209 G210 Y233
Binding residue
(residue number reindexed from 1)
N71 Y73 V74 E121 S122 Y123 E174 R177 E206 W209 G210 Y233
Annotation score1
Binding affinityMOAD: Ki=7.5nM
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

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Molecular Function

View graph for
Biological Process
External links
PDB RCSB:3hiv, PDBe:3hiv, PDBj:3hiv
PDBsum3hiv
PubMed19920175
UniProtQ2QEH4

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