Np mrd loader

Record Information
Version2.0
Created at2022-09-05 14:02:44 UTC
Updated at2022-09-05 14:02:44 UTC
NP-MRD IDNP0214674
Secondary Accession NumbersNone
Natural Product Identification
Common Namen-[(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
DescriptionPyridomycin 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).
Structure
Thumb
SynonymsNot Available
Chemical FormulaC27H32N4O8
Average Mass540.5730 Da
Monoisotopic Mass540.22201 Da
IUPAC NameN-[(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
Traditional NameN-[(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
CAS Registry NumberNot Available
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
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-
InChI KeyWHIKSLGSXKIHCA-UCQKPKSFSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Streptomyces pyridomyceticusLOTUS Database
Chemical Taxonomy
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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassPeptidomimetics
Sub ClassDepsipeptides
Direct ParentCyclic depsipeptides
Alternative Parents
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
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP2.36ChemAxon
pKa (Strongest Acidic)1.22ChemAxon
pKa (Strongest Basic)4.92ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area184.02 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity138.82 m³·mol⁻¹ChemAxon
Polarizability55.06 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID4572417
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5458474
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. 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 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]
  5. 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 ]
  6. LOTUS database [Link]