Structure of PDB 1rf2 Chain D Binding Site BS01

Receptor Information

>1rf2 Chain D (length=103) Species: 666 (Vibrio cholerae)

TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQV
EVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAIS
MAN

Ligand information

• Ligand ID: BV4
• InChI: InChI=1S/C79H123N15O32/c80-53(49-121-78(109)87-15-7-31-117-35-39-119-37-33-115-29-5-13-83-62-60(66(99)68(62)101)81-9-1-17-89-21-25-91(26-22-89)19-3-11-85-74(107)51-41-54(93(111)112)45-56(43-51)123-76-72(105)70(103)64(97)58(47-95)125-76)50-122-79(110)88-16-8-32-118-36-40-120-38-34-116-30-6-14-84-63-61(67(100)69(63)102)82-10-2-18-90-23-27-92(28-24-90)20-4-12-86-75(108)52-42-55(94(113)114)46-57(44-52)124-77-73(106)71(104)65(98)59(48-96)126-77/h41-46,53,58-59,64-65,70-73,76-77,81-84,95-98,103-106H,1-40,47-50,80H2,(H,85,107)(H,86,108)(H,87,109)(H,88,110)/t53?,58-,59?,64+,65?,70+,71?,72-,73?,76+,77?/m1/s1
• InChIKey: BPHYTQORKHDHAH-OHNHNXIVSA-N
• SMILES:
  CACTVS 3.341: NC(COC(=O)NCCCOCCOCCOCCCNC1=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)NCCCOCCOCCOCCCNC5=C(NCCCN6CCN(CCCNC(=O)c7cc(OC8OC(CO)C(O)C(O)C8O)cc(c7)[N+]([O-])=O)CC6)C(=O)C5=O
  ACDLabs 10.04: O=C4C(NCCCN1CCN(CC1)CCCNC(=O)c3cc([N+]([O-])=O)cc(OC2OC(CO)C(O)C(O)C2O)c3)=C(C4=O)NCCCOCCOCCOCCCNC(=O)OCC(N)COC(=O)NCCCOCCOCCOCCCNC=5C(=O)C(=O)C=5NCCCN6CCN(CC6)CCCNC(=O)c8cc(OC7OC(C(O)C(O)C7O)CO)cc([N+]([O-])=O)c8
  OpenEye OEToolkits 1.5.0: c1c(cc(cc1[N+](=O)[O-])OC2C(C(C(C(O2)CO)O)O)O)C(=O)NCCCN3CCN(CC3)CCCNC4=C(C(=O)C4=O)NCCCOCCOCCOCCCNC(=O)OCC(COC(=O)NCCCOCCOCCOCCCNC5=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 1.5.0: c1c(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)NCCCOCCOCCOCCCNC(=O)OCC(COC(=O)NCCCOCCOCCOCCCNC5=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 3.341: NC(COC(=O)NCCCOCCOCCOCCCNC1=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)NCCCOCCOCCOCCCNC5=C(NCCCN6CCN(CCCNC(=O)c7cc(OC8OC(CO)C(O)C(O)C8O)cc(c7)[N+]([O-])=O)CC6)C(=O)C5=O
• Formula: C79 H123 N15 O32
• Name: 1,3-BIS-([3-[3-[3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYLAMINO-3,4-DIOXO-CYCLOBUTENYL]-AMINO-PROPOXY-ETHOXY-ETHOXY]-PROPYL-]AMINO-CARBONYLOXY)-2-AMINO-PROPANE;
  BV4
• DrugBank: DB02572
• PDB chain: 1rf2 Chain D Residue 104

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1rf2 Nonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer.
• Resolution: 1.35 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 score: 1
• Binding affinity: MOAD: ic50=17uM

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

External links

• PDB: RCSB:1rf2, PDBe:1rf2, PDBj:1rf2
• PDBsum: 1rf2
• PubMed: 15380181
• UniProt: P01556|CHTB_VIBCH Cholera enterotoxin subunit B (Gene Name=ctxB)