Structure of PDB 1rdp Chain F Binding Site BS01

Receptor Information
>1rdp 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 IDBV3
InChIInChI=1S/C63H91N15O26/c64-37(33-99-62(93)71-11-9-67-46-44(50(83)52(46)85)65-5-1-13-73-17-21-75(22-18-73)15-3-7-69-58(91)35-25-38(77(95)96)29-40(27-35)101-60-56(89)54(87)48(81)42(31-79)103-60)34-100-63(94)72-12-10-68-47-45(51(84)53(47)86)66-6-2-14-74-19-23-76(24-20-74)16-4-8-70-59(92)36-26-39(78(97)98)30-41(28-36)102-61-57(90)55(88)49(82)43(32-80)104-61/h25-30,37,42-43,48-49,54-57,60-61,65-68,79-82,87-90H,1-24,31-34,64H2,(H,69,91)(H,70,92)(H,71,93)(H,72,94)/t37?,42-,43?,48+,49?,54+,55?,56-,57?,60+,61?/m1/s1
InChIKeyHQTVCYHBYUXJDJ-ISUJOEFPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(COC(=O)NCCNC1=C(NCCCN2CCN(CCCNC(=O)c3cc(O[C@H]4O[C@H](CO)[C@H](O)[C@H](O)[C@H]4O)cc(c3)[N+]([O-])=O)CC2)C(=O)C1=O)COC(=O)NCCNC5=C(NCCCN6CCN(CCCNC(=O)c7cc(OC8OC(CO)C(O)C(O)C8O)cc(c7)[N+]([O-])=O)CC6)C(=O)C5=O
OpenEye OEToolkits 1.5.0c1c(cc(cc1[N+](=O)[O-])OC2C(C(C(C(O2)CO)O)O)O)C(=O)NCCCN3CCN(CC3)CCCNC4=C(C(=O)C4=O)NCCNC(=O)OCC(COC(=O)NCCNC5=C(C(=O)C5=O)NCCCN6CCN(CC6)CCCNC(=O)c7cc(cc(c7)OC8C(C(C(C(O8)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)CCCNC4=C(C(=O)C4=O)NCCNC(=O)OCC(COC(=O)NCCNC5=C(C(=O)C5=O)NCCCN6CCN(CC6)CCCNC(=O)c7cc(cc(c7)O[C@@H]8[C@@H]([C@@H]([C@@H]([C@@H](O8)CO)O)O)O)[N+](=O)[O-])N
CACTVS 3.341NC(COC(=O)NCCNC1=C(NCCCN2CCN(CCCNC(=O)c3cc(O[CH]4O[CH](CO)[CH](O)[CH](O)[CH]4O)cc(c3)[N+]([O-])=O)CC2)C(=O)C1=O)COC(=O)NCCNC5=C(NCCCN6CCN(CCCNC(=O)c7cc(OC8OC(CO)C(O)C(O)C8O)cc(c7)[N+]([O-])=O)CC6)C(=O)C5=O
ACDLabs 10.04O=[N+]([O-])c2cc(cc(OC1OC(CO)C(O)C(O)C1O)c2)C(=O)NCCCN3CCN(CC3)CCCNC=4C(=O)C(=O)C=4NCCNC(=O)OCC(N)COC(=O)NCCNC=5C(=O)C(=O)C=5NCCCN6CCN(CC6)CCCNC(=O)c8cc(OC7OC(C(O)C(O)C7O)CO)cc([N+]([O-])=O)c8
FormulaC63 H91 N15 O26
Name1,3-BIS-([[3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYLAMINO-3,4-DIOXO-CYCLOBU TENYL]-AMINO-ETHYL]-AMINO-CARBONYLOXY)-2-AMINO-PROPANE;
BV3
ChEMBL
DrugBankDB02903
ZINC
PDB chain1rdp Chain F Residue 106 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1rdp Nonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer.
Resolution1.35 Å
Binding residue
(original residue number in PDB)		Y12 E51 Q56 H57 Q61 W88 N90 K91
Binding residue
(residue number reindexed from 1)		Y12 E51 Q56 H57 Q61 W88 N90 K91
Annotation score1
Binding affinityMOAD: ic50=9uM
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1rdp, PDBe:1rdp, PDBj:1rdp
PDBsum1rdp
PubMed15380181
UniProtP01556|CHTB_VIBCH Cholera enterotoxin subunit B (Gene Name=ctxB)

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