Structure of PDB 1rcv Chain F Binding Site BS01

Receptor Information
>1rcv 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 IDBV1
InChIInChI=1S/C50H72N10O20/c61-27-35-39(63)43(67)45(69)49(79-35)77-33-23-29(21-31(25-33)59(73)74)47(71)53-7-3-11-57-17-13-55(14-18-57)9-1-5-51-37-38(42(66)41(37)65)52-6-2-10-56-15-19-58(20-16-56)12-4-8-54-48(72)30-22-32(60(75)76)26-34(24-30)78-50-46(70)44(68)40(64)36(28-62)80-50/h21-26,35-36,39-40,43-46,49-52,61-64,67-70H,1-20,27-28H2,(H,53,71)(H,54,72)/t35-,36?,39+,40?,43+,44?,45-,46?,49+,50?/m1/s1
InChIKeyWWGXKLSKKKQRMN-MLHPNDMTSA-N
SMILES
SoftwareSMILES
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)NCCCN5CCN(CC5)CCCNC(=O)c6cc(cc(c6)OC7C(C(C(C(O7)CO)O)O)O)[N+](=O)[O-]
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)NCCCN5CCN(CC5)CCCNC(=O)c6cc(cc(c6)O[C@@H]7[C@@H]([C@@H]([C@@H]([C@@H](O7)CO)O)O)O)[N+](=O)[O-]
ACDLabs 10.04[O-][N+](=O)c2cc(cc(OC1OC(CO)C(O)C(O)C1O)c2)C(=O)NCCCN3CCN(CC3)CCCNC=4C(=O)C(=O)C=4NCCCN5CCN(CC5)CCCNC(=O)c7cc(OC6OC(C(O)C(O)C6O)CO)cc([N+]([O-])=O)c7
CACTVS 3.341OC[C@H]1O[C@H](Oc2cc(cc(c2)[N+]([O-])=O)C(=O)NCCCN3CCN(CCCNC4=C(NCCCN5CCN(CCCNC(=O)c6cc(OC7OC(CO)C(O)C(O)C7O)cc(c6)[N+]([O-])=O)CC5)C(=O)C4=O)CC3)[C@H](O)[C@@H](O)[C@H]1O
CACTVS 3.341OC[CH]1O[CH](Oc2cc(cc(c2)[N+]([O-])=O)C(=O)NCCCN3CCN(CCCNC4=C(NCCCN5CCN(CCCNC(=O)c6cc(OC7OC(CO)C(O)C(O)C7O)cc(c6)[N+]([O-])=O)CC5)C(=O)C4=O)CC3)[CH](O)[CH](O)[CH]1O
FormulaC50 H72 N10 O20
Name[3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYLAMINO] -2-(3-{4-[3-(3-NITRO-5-[GALACTOPYRANOSYLOXY]-BENZOYLAMINO)-PROPYL]-PIPERAZIN-1-YL} -PROPYL-AMINO)-3,4-DIOXO-CYCLOBUTENE;
BV1
ChEMBL
DrugBankDB04210
ZINC
PDB chain1rcv 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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PDB1rcv Nonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		G33 R35
Binding residue
(residue number reindexed from 1)		G33 R35
Annotation score1
Binding affinityMOAD: ic50=29uM
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1rcv, PDBe:1rcv, PDBj:1rcv
PDBsum1rcv
PubMed15380181
UniProtP01556|CHTB_VIBCH Cholera enterotoxin subunit B (Gene Name=ctxB)

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