Structure of PDB 1g9b Chain A Binding Site BS03

Receptor Information
>1g9b Chain A (length=1287) Species: 1491 (Clostridium botulinum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKITDRIWIIPERYT
FGYKPEDFNKSSGIFNRDVCEYYDPDYLNTNDKKNIFLQTMIKLFNRIKS
KPLGEKLLEMIINGIPYLGDRRVPLEEFNTNIASVTVNKLISNPGEVERK
KGIFANLIIFGPGPVLNENETIDIGIQNHFASREGFGGIMQMKFCPEYVS
VFNNVQENKGASIFNRRGYFSDPALILMHELIHVLHGLYGIKVDDLPIVP
NEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYDKVLQNFRGIVD
RLNKVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESFDKLYKS
LMFGFTETNIAENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNIS
DKDMEKEYRGQNKAINKQAYEEISKEHLAVYKIQMCKSVGICIDVDNEDL
FFIADKNSFSDDLSKNERIEYNTQSNYIENDFPINELILDTDLISKIELP
SENTESLTDFNVDVPVYEKQPAIKKIFTDENTIFQYLYSQTFPLDIRDIS
LTSSFDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAGWVKQIVNDFVIE
ANKSNTMDKIADISLIVPYIGLALNVGNETAKGNFENAFEIAGASILLEF
IPELLIPVVGAFLLESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIVAQW
LSTVNTQFYTIKEGMYKALNYQAQALEEIIKYRYNIYSEKEKSNINIDFN
DINSKLNEGINQAIDNINNFINGCSVSYLMKKMIPLAVEKLLDFDNTLKK
NLLNYIDENKLYLIGSAEYEKSKVNKYLKTIMPFDLSIYTNDTILIEMFN
KYNSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSS
ANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIIN
CMKNNSGWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFF
VTITNNLNNAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFI
WMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAG
NKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNSQ
SINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEF
YNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYK
DYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTE
Ligand information
Ligand IDBAB
InChIInChI=1S/C17H16N8/c18-16(19)8-1-3-10-12(5-8)24-14(22-10)7-15-23-11-4-2-9(17(20)21)6-13(11)25-15/h1-6H,7H2,(H3,18,19)(H3,20,21)(H,22,24)(H,23,25)/p+3
InChIKeyQZKOOEFIMWKZPK-UHFFFAOYSA-Q
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc2c(cc1C(=[NH2+])N)[nH]c([nH+]2)Cc3[nH]c4cc(ccc4n3)C(=[NH2+])N
ACDLabs 10.04n2c1ccc(cc1nc2Cc4[nH+]c3ccc(C(=[NH2+])\N)cc3n4)\C(=[NH2+])N
CACTVS 3.341NC(=[NH2+])c1ccc2nc(Cc3[nH]c4cc(ccc4[nH+]3)C(N)=[NH2+])[nH]c2c1
FormulaC17 H19 N8
NameBIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE
ChEMBL
DrugBankDB01705
ZINC
PDB chain1g9b Chain A Residue 1293 [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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PDB1g9b A Novel Mechanism for Clostridium botulinum Neurotoxin Inhibition
Resolution2.0 Å
Binding residue
(original residue number in PDB)		N203 R217 D375 L377 D452 F537 L540 E716 K720 Y724
Binding residue
(residue number reindexed from 1)		N203 R217 D375 L377 D449 F534 L537 E713 K717 Y721
Annotation score1
Binding affinityMOAD: ic50~7.5uM
PDBbind-CN: -logKd/Ki=5.30,IC50=5uM
Enzymatic activity
Catalytic site (original residue number in PDB) H229 E230 H233 E267 R369
Catalytic site (residue number reindexed from 1) H229 E230 H233 E267 R369
Enzyme Commision number 3.4.24.69: bontoxilysin.
Gene Ontology
Molecular Function
GO:0004222 metalloendopeptidase activity
GO:0005515 protein binding
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
GO:0008289 lipid binding
GO:0008320 protein transmembrane transporter activity
GO:0046872 metal ion binding
GO:0090729 toxin activity
Biological Process
GO:0006508 proteolysis
GO:0035821 modulation of process of another organism
GO:0071806 protein transmembrane transport
Cellular Component
GO:0005576 extracellular region
GO:0016020 membrane
GO:0020002 host cell plasma membrane
GO:0030430 host cell cytoplasm
GO:0044161 host cell cytoplasmic vesicle
GO:0044164 host cell cytosol
GO:0044221 host cell synapse
GO:0044231 host cell presynaptic membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1g9b, PDBe:1g9b, PDBj:1g9b
PDBsum1g9b
PubMed12146945
UniProtP10844|BXB_CLOBO Botulinum neurotoxin type B (Gene Name=botB)

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