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ubonodin   Click here for help

GtoPdb Ligand ID: 14235

Compound class: Peptide
Comment: Ubonodin is an antimicrobial lasso peptide discovered using genome mining in Burkholderia ubonensis [1]. It inhibits bacterial RNA polymerase in vitro and has activity against B. multivorans and B. cepacia, opportunistic bacterial pathogens that can cause lung infections in cystic fibrosis patients.
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES CC[C@H](C)[C@H]1C(=O)N[C@@H](C)C(=O)N[C@@H](CCC(=O)NCC(=O)NCC(=O)N[C@@H](CC(=O)O)C(=O)NCC(=O)N[C@@H](CO)C(=O)N1)C(=O)N[C@@H](CC2=CC=C(C=C2)O)C(=O)N[C@@H](CC3=CC=CC=C3)C(=O)N[C@@H](CC(=O)N)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N4CCC[C@H]4C(=O)N[C@@H](CCSC)C(=O)N[C@@H](CC5=CNC=N5)C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CC6=CNC=N6)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](CC7=CNC8=C7C=CC=C8)C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CCSC)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](CO)C(=O)NCC(=O)N[C@@H](CC9=CC=C(C=C9)O)C(=O)N[C@@H](CC%10=CC=C(C=C%10)O)C(=O)NCC(=O)O
Isomeric SMILES CC[C@H](C)[C@H]1C(=O)N[C@H](C(=O)N[C@@H](CCC(=O)NCC(=O)NCC(=O)N[C@H](C(=O)NCC(=O)N[C@H](C(=O)N1)CO)CC(=O)O)C(=O)N[C@@H](CC2=CC=C(C=C2)O)C(=O)N[C@@H](CC3=CC=CC=C3)C(=O)N[C@@H](CC(=O)N)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N4CCC[C@H]4C(=O)N[C@@H](CCSC)C(=O)N[C@@H](CC5=CNC=N5)C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CC6=CNC=N6)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](CC7=CNC8=CC=CC=C87)C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CCSC)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](CO)C(=O)NCC(=O)N[C@@H](CC9=CC=C(C=C9)O)C(=O)N[C@@H](CC%10=CC=C(C=C%10)O)C(=O)NCC(=O)O)C
InChI InChI=1S/C143H196N38O43S2/c1-10-71(4)117-139(221)159-74(7)120(202)163-88(39-41-108(189)152-62-109(190)153-63-110(191)161-100(56-113(194)195)122(204)154-65-112(193)162-104(68-183)137(219)180-117)124(206)169-95(51-78-30-36-84(186)37-31-78)129(211)170-94(48-75-20-14-13-15-21-75)130(212)173-99(55-107(145)188)133(215)167-91(24-18-44-150-143(146)147)142(224)181-45-19-25-105(181)138(220)165-89(42-46-225-8)125(207)172-98(54-81-61-149-70-158-81)136(218)179-119(73(6)12-3)141(223)176-97(53-80-60-148-69-157-80)132(214)175-101(57-114(196)197)134(216)171-96(52-79-59-151-86-23-17-16-22-85(79)86)131(213)164-87(38-40-106(144)187)127(209)178-118(72(5)11-2)140(222)166-90(43-47-226-9)126(208)174-102(58-115(198)199)135(217)177-103(67-182)123(205)155-64-111(192)160-93(50-77-28-34-83(185)35-29-77)128(210)168-92(121(203)156-66-116(200)201)49-76-26-32-82(184)33-27-76/h13-17,20-23,26-37,59-61,69-74,87-105,117-119,151,182-186H,10-12,18-19,24-25,38-58,62-68H2,1-9H3,(H2,144,187)(H2,145,188)(H,148,157)(H,149,158)(H,152,189)(H,153,190)(H,154,204)(H,155,205)(H,156,203)(H,159,221)(H,160,192)(H,161,191)(H,162,193)(H,163,202)(H,164,213)(H,165,220)(H,166,222)(H,167,215)(H,168,210)(H,169,206)(H,170,211)(H,171,216)(H,172,207)(H,173,212)(H,174,208)(H,175,214)(H,176,223)(H,177,217)(H,178,209)(H,179,218)(H,180,219)(H,194,195)(H,196,197)(H,198,199)(H,200,201)(H4,146,147,150)/t71-,72-,73-,74-,87-,88-,89-,90-,91-,92-,93-,94-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,117-,118-,119-/m0/s1
InChI Key AELLOIFPDIOLRK-KHQMEOLFSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
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Mechanism Of Action and Pharmacodynamic Effects Click here for help
Ubonodin inhibits RNA polymerase, with a narrow and selective spectrum of antibacterial activity that is determined by cellular uptake of the compound. The transport pathway of ubonodin in Burkholderia has been elucidated, with the TonB-dependent transporter PupB identified as the outer membrane receptor and YddA, a putative ATP-binding cassette (ABC) transporter, the inner membrane receptor [2].