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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/)
References
1. Cheung-Lee WL, Parry ME, Zong C, Cartagena AJ, Darst SA, Connell ND, Russo R, Link AJ. (2020)
Discovery of Ubonodin, an Antimicrobial Lasso Peptide Active against Members of the Burkholderia cepacia Complex.
Chembiochem, 21 (9): 1335-1340. [PMID:31765515]
2. Do T, Thokkadam A, Leach R, Link AJ. (2022)
Phenotype-Guided Comparative Genomics Identifies the Complete Transport Pathway of the Antimicrobial Lasso Peptide Ubonodin in Burkholderia.
ACS Chem Biol, 17 (8): 2332-2343. [PMID:35802499]