| Record Information |
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| Version | 2.0 |
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| Created at | 2022-09-05 14:02:44 UTC |
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| Updated at | 2022-09-05 14:02:44 UTC |
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| NP-MRD ID | NP0214674 |
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| Secondary Accession Numbers | None |
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| Natural Product Identification |
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| Common Name | n-[(2z)-2-(butan-2-ylidene)-7,10-dihydroxy-5,11-dimethyl-3,12-dioxo-9-(pyridin-3-ylmethyl)-1,4-dioxa-8-azacyclododec-7-en-6-yl]-3-hydroxypyridine-2-carboximidic acid |
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| Description | Pyridomycin belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. n-[(2z)-2-(butan-2-ylidene)-7,10-dihydroxy-5,11-dimethyl-3,12-dioxo-9-(pyridin-3-ylmethyl)-1,4-dioxa-8-azacyclododec-7-en-6-yl]-3-hydroxypyridine-2-carboximidic acid is found in Streptomyces pyridomyceticus. n-[(2z)-2-(butan-2-ylidene)-7,10-dihydroxy-5,11-dimethyl-3,12-dioxo-9-(pyridin-3-ylmethyl)-1,4-dioxa-8-azacyclododec-7-en-6-yl]-3-hydroxypyridine-2-carboximidic acid was first documented in 2014 (PMID: 24292073). Based on a literature review a small amount of articles have been published on Pyridomycin (PMID: 35108072) (PMID: 34705221) (PMID: 31904960) (PMID: 27197800). |
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| Structure | CC\C(C)=C1/OC(=O)C(C)C(O)C(CC2=CC=CN=C2)N=C(O)C(N=C(O)C2=NC=CC=C2O)C(C)OC1=O InChI=1S/C27H32N4O8/c1-5-14(2)23-27(37)38-16(4)20(31-25(35)21-19(32)9-7-11-29-21)24(34)30-18(12-17-8-6-10-28-13-17)22(33)15(3)26(36)39-23/h6-11,13,15-16,18,20,22,32-33H,5,12H2,1-4H3,(H,30,34)(H,31,35)/b23-14- |
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| Synonyms | Not Available |
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| Chemical Formula | C27H32N4O8 |
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| Average Mass | 540.5730 Da |
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| Monoisotopic Mass | 540.22201 Da |
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| IUPAC Name | N-[(2Z)-2-(butan-2-ylidene)-7,10-dihydroxy-5,11-dimethyl-3,12-dioxo-9-[(pyridin-3-yl)methyl]-1,4-dioxa-8-azacyclododec-7-en-6-yl]-3-hydroxypyridine-2-carboximidic acid |
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| Traditional Name | N-[(2Z)-2-(butan-2-ylidene)-7,10-dihydroxy-5,11-dimethyl-3,12-dioxo-9-(pyridin-3-ylmethyl)-1,4-dioxa-8-azacyclododec-7-en-6-yl]-3-hydroxypyridine-2-carboximidic acid |
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| CAS Registry Number | Not Available |
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| SMILES | CC\C(C)=C1/OC(=O)C(C)C(O)C(CC2=CC=CN=C2)N=C(O)C(N=C(O)C2=NC=CC=C2O)C(C)OC1=O |
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| InChI Identifier | InChI=1S/C27H32N4O8/c1-5-14(2)23-27(37)38-16(4)20(31-25(35)21-19(32)9-7-11-29-21)24(34)30-18(12-17-8-6-10-28-13-17)22(33)15(3)26(36)39-23/h6-11,13,15-16,18,20,22,32-33H,5,12H2,1-4H3,(H,30,34)(H,31,35)/b23-14- |
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| InChI Key | WHIKSLGSXKIHCA-UCQKPKSFSA-N |
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| Experimental Spectra |
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| Not Available | | Predicted Spectra |
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| | Spectrum Type | Description | Depositor ID | Depositor Organization | Depositor | Deposition Date | View |
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| 1D NMR | 13C NMR Spectrum (1D, 25 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 100 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 252 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 1000 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 50 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 200 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 75 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 300 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 101 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 400 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 126 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 500 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 151 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 600 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 176 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 700 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 201 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 800 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 13C NMR Spectrum (1D, 226 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum | | 1D NMR | 1H NMR Spectrum (1D, 900 MHz, H2O, predicted) | Wishart Lab | Wishart Lab | David Wishart | 2021-06-20 | View Spectrum |
| | Chemical Shift Submissions |
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| Not Available | | Species |
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| Species of Origin | |
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| Chemical Taxonomy |
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| Description | Belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. |
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| Kingdom | Organic compounds |
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| Super Class | Organic acids and derivatives |
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| Class | Peptidomimetics |
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| Sub Class | Depsipeptides |
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| Direct Parent | Cyclic depsipeptides |
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| Alternative Parents | |
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| Substituents | - Cyclic depsipeptide
- Macrolactam
- N-acyl-alpha amino acid or derivatives
- Alpha-amino acid or derivatives
- Pyridinecarboxamide
- Pyridine carboxylic acid or derivatives
- 2-heteroaryl carboxamide
- Hydroxypyridine
- Dicarboxylic acid or derivatives
- Pyridine
- Vinylogous acid
- Alpha,beta-unsaturated carboxylic ester
- Enoate ester
- Heteroaromatic compound
- Enol ester
- Secondary carboxylic acid amide
- Secondary alcohol
- Carboxamide group
- Carboxylic acid ester
- Lactone
- Lactam
- Organoheterocyclic compound
- Oxacycle
- Azacycle
- Carboxylic acid derivative
- Organic nitrogen compound
- Organopnictogen compound
- Alcohol
- Organic oxygen compound
- Organic oxide
- Organonitrogen compound
- Organooxygen compound
- Carbonyl group
- Hydrocarbon derivative
- Aromatic heteromonocyclic compound
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| Molecular Framework | Aromatic heteromonocyclic compounds |
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| External Descriptors | Not Available |
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| Physical Properties |
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| State | Not Available |
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| Experimental Properties | | Property | Value | Reference |
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| Melting Point | Not Available | Not Available | | Boiling Point | Not Available | Not Available | | Water Solubility | Not Available | Not Available | | LogP | Not Available | Not Available |
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| Predicted Properties | |
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| General References | - Huang T, Zhou Z, Wei M, Chen L, Xiao Z, Deng Z, Lin S: Characterization of Pyridomycin B Reveals the Formation of Functional Groups in Antimycobacterial Pyridomycin. Appl Environ Microbiol. 2022 Mar 22;88(6):e0203521. doi: 10.1128/AEM.02035-21. Epub 2022 Feb 2. [PubMed:35108072 ]
- Luo L, Yang J, Wang C, Wu J, Li Y, Zhang X, Li H, Zhang H, Zhou Y, Lu A, Chen S: Natural products for infectious microbes and diseases: an overview of sources, compounds, and chemical diversities. Sci China Life Sci. 2022 Jun;65(6):1123-1145. doi: 10.1007/s11427-020-1959-5. Epub 2021 Oct 21. [PubMed:34705221 ]
- Kienle M, Eisenring P, Stoessel B, Horlacher OP, Hasler S, van Colen G, Hartkoorn RC, Vocat A, Cole ST, Altmann KH: Synthesis and Structure-Activity Relationship Studies of C2-Modified Analogs of the Antimycobacterial Natural Product Pyridomycin. J Med Chem. 2020 Feb 13;63(3):1105-1131. doi: 10.1021/acs.jmedchem.9b01457. Epub 2020 Jan 21. [PubMed:31904960 ]
- Huang T, Li L, Brock NL, Deng Z, Lin S: Functional Characterization of PyrG, an Unusual Nonribosomal Peptide Synthetase Module from the Pyridomycin Biosynthetic Pathway. Chembiochem. 2016 Aug 3;17(15):1421-5. doi: 10.1002/cbic.201600156. Epub 2016 Jun 9. [PubMed:27197800 ]
- Hartkoorn RC, Pojer F, Read JA, Gingell H, Neres J, Horlacher OP, Altmann KH, Cole ST: Pyridomycin bridges the NADH- and substrate-binding pockets of the enoyl reductase InhA. Nat Chem Biol. 2014 Feb;10(2):96-8. doi: 10.1038/nchembio.1405. Epub 2013 Dec 1. [PubMed:24292073 ]
- LOTUS database [Link]
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