Structure of PDB 1rd9 Chain F Binding Site BS01

Receptor Information
>1rd9 Chain F (length=103) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQV
EVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAIS
MAN
Ligand information
Ligand IDBV2
InChIInChI=1S/C51H79N11O22/c52-33(29-79-50(73)55-7-3-11-59-17-13-57(14-18-59)9-1-5-53-46(71)31-21-34(61(75)76)25-36(23-31)81-48-44(69)42(67)40(65)38(27-63)83-48)30-80-51(74)56-8-4-12-60-19-15-58(16-20-60)10-2-6-54-47(72)32-22-35(62(77)78)26-37(24-32)82-49-45(70)43(68)41(66)39(28-64)84-49/h21-26,33,38-45,48-49,63-70H,1-20,27-30,52H2,(H,53,71)(H,54,72)(H,55,73)(H,56,74)/t33?,38-,39?,40+,41?,42+,43?,44-,45?,48+,49?/m1/s1
InChIKeyRJLCAAJYVGPDFG-LNGNCPBTSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(COC(=O)NCCCN1CCN(CCCNC(=O)c2cc(O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)cc(c2)[N+]([O-])=O)CC1)COC(=O)NCCCN4CCN(CCCNC(=O)c5cc(OC6OC(CO)C(O)C(O)C6O)cc(c5)[N+]([O-])=O)CC4
ACDLabs 10.04[O-][N+](=O)c2cc(cc(OC1OC(CO)C(O)C(O)C1O)c2)C(=O)NCCCN3CCN(CC3)CCCNC(=O)OCC(N)COC(=O)NCCCN4CCN(CC4)CCCNC(=O)c6cc(OC5OC(C(O)C(O)C5O)CO)cc([N+]([O-])=O)c6
OpenEye OEToolkits 1.5.0c1c(cc(cc1[N+](=O)[O-])OC2C(C(C(C(O2)CO)O)O)O)C(=O)NCCCN3CCN(CC3)CCCNC(=O)OCC(COC(=O)NCCCN4CCN(CC4)CCCNC(=O)c5cc(cc(c5)OC6C(C(C(C(O6)CO)O)O)O)[N+](=O)[O-])N
OpenEye OEToolkits 1.5.0c1c(cc(cc1[N+](=O)[O-])O[C@@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)O)O)C(=O)NCCCN3CCN(CC3)CCCNC(=O)OCC(COC(=O)NCCCN4CCN(CC4)CCCNC(=O)c5cc(cc(c5)O[C@@H]6[C@@H]([C@@H]([C@@H]([C@@H](O6)CO)O)O)O)[N+](=O)[O-])N
CACTVS 3.341NC(COC(=O)NCCCN1CCN(CCCNC(=O)c2cc(O[C@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)cc(c2)[N+]([O-])=O)CC1)COC(=O)NCCCN4CCN(CCCNC(=O)c5cc(OC6OC(CO)C(O)C(O)C6O)cc(c5)[N+]([O-])=O)CC4
FormulaC51 H79 N11 O22
Name1,3-BIS-([3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYL-AMINO]-CARBONYLOXY)-2-AMINO-PROPANE;
BV2
ChEMBL
DrugBankDB02574
ZINC
PDB chain1rd9 Chain E Residue 105 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1rd9 Nonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer.
Resolution1.44 Å
Binding residue
(original residue number in PDB)		G33 R35
Binding residue
(residue number reindexed from 1)		G33 R35
Annotation score1
Binding affinityMOAD: ic50=13uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005534 galactose binding
GO:0046812 host cell surface binding
GO:0090729 toxin activity
Biological Process
GO:0035821 modulation of process of another organism
GO:0042531 positive regulation of tyrosine phosphorylation of STAT protein
Cellular Component
GO:0005576 extracellular region
GO:0016020 membrane
GO:0020002 host cell plasma membrane
GO:0042597 periplasmic space
GO:1902494 catalytic complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1rd9, PDBe:1rd9, PDBj:1rd9
PDBsum1rd9
PubMed15380181
UniProtP01556|CHTB_VIBCH Cholera enterotoxin subunit B (Gene Name=ctxB)

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