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Record Information
Version1.0
Created at2020-12-09 06:31:31 UTC
Updated at2021-07-15 17:02:12 UTC
NP-MRD IDNP0009060
Secondary Accession NumbersNone
Natural Product Identification
Common NameHelvecardin A
Provided ByNPAtlasNPAtlas Logo
DescriptionHelvecardin A belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. Helvecardin A is found in Pseudonocardia, Pseudonocardia compacta and Pseudonocardia compacta subsp. helvetica. It was first documented in 1991 (PMID: 2026551). Based on a literature review very few articles have been published on Helvecardin A (PMID: 2026550).
Structure
Thumb
Synonyms
ValueSource
(1S,2R,18S,19S,22S,25R,28R)-2-{[(2R,4R,5R,6R)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-48-{[(2R,3R,4R,5S,6R)-3-{[(2R,4R,5R,6R)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-chloro-22-(3-chloro-4-hydroxyphenyl)-19-{[(2R)-2-(4-{[(2S,3S,4S,5S,6R)-4,5-dihydroxy-3-methoxy-6-methyloxan-2-yl]oxy}phenyl)-1-hydroxy-2-(methylamino)ethylidene]amino}-20,23,26,32,35,37,42,44-octahydroxy-18-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-7,13-dioxa-21,24,27,41,43-pentaazaoctacyclo[26.14.2.2,.2,.1,.1,.0,.0,]pentaconta-3,5,8,10,12(48),14,16,20,23,26,29(45),30,32,34(39),35,37,41,43,46,49-icosaene-40-carboxylateGenerator
Chemical FormulaC90H103Cl2N9O36
Average Mass1957.7400 Da
Monoisotopic Mass1955.58828 Da
IUPAC Name(1S,2R,18S,19S,22S,28R,40S)-2-{[(2R,4R,5R,6R)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-48-{[(2R,3R,4R,5S,6R)-3-{[(2R,4R,5R,6R)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-49-chloro-22-(3-chloro-4-hydroxyphenyl)-19-[(2R)-2-(4-{[(2S,3S,4S,5S,6R)-4,5-dihydroxy-3-methoxy-6-methyloxan-2-yl]oxy}phenyl)-2-(methylamino)acetamido]-32,35,37-trihydroxy-20,23,26,42,44-pentaoxo-18-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-7,13-dioxa-21,24,27,41,43-pentaazaoctacyclo[26.14.2.2^{3,6}.2^{14,17}.1^{8,12}.1^{29,33}.0^{10,25}.0^{34,39}]pentaconta-3,5,8(48),9,11,14,16,29,31,33(45),34,36,38,46,49-pentadecaene-40-carboxylic acid
Traditional Name(1S,2R,18S,19S,22S,28R,40S)-2-{[(2R,4R,5R,6R)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-48-{[(2R,3R,4R,5S,6R)-3-{[(2R,4R,5R,6R)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-49-chloro-22-(3-chloro-4-hydroxyphenyl)-19-[(2R)-2-(4-{[(2S,3S,4S,5S,6R)-4,5-dihydroxy-3-methoxy-6-methyloxan-2-yl]oxy}phenyl)-2-(methylamino)acetamido]-32,35,37-trihydroxy-20,23,26,42,44-pentaoxo-18-{[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-7,13-dioxa-21,24,27,41,43-pentaazaoctacyclo[26.14.2.2^{3,6}.2^{14,17}.1^{8,12}.1^{29,33}.0^{10,25}.0^{34,39}]pentaconta-3,5,8(48),9,11,14,16,29,31,33(45),34,36,38,46,49-pentadecaene-40-carboxylic acid
CAS Registry NumberNot Available
SMILES
CN[C@@H](C(=O)N[C@H]1[C@@H](O[C@@H]2O[C@@H](CO)[C@H](O)[C@@H](O)[C@@H]2O)C2=CC=C(OC3=CC4=CC(OC5=C(Cl)C=C(C=C5)[C@@H](O[C@H]5C[C@@H](N)[C@@H](O)[C@@H](C)O5)[C@@H]5NC(=O)[C@H](NC(=O)[C@@H]4NC(=O)[C@@H](NC1=O)C1=CC(Cl)=C(O)C=C1)C1=CC(=C(O)C=C1)C1=C(O)C=C(O)C=C1C(NC5=O)C(O)=O)=C3O[C@H]1O[C@H](CO)[C@@H](O)[C@@H](O)[C@H]1O[C@@H]1C[C@@H](N)[C@@H](O)[C@@H](C)O1)C=C2)C1=CC=C(O[C@@H]2O[C@H](C)[C@@H](O)[C@H](O)[C@@H]2OC)C=C1
InChI Identifier
InChI=1S/C90H103Cl2N9O36/c1-31-67(108)47(93)27-57(126-31)134-77-38-12-19-52(46(92)22-38)131-54-24-39-23-53(78(54)137-90-80(74(115)71(112)56(30-103)133-90)135-58-28-48(94)68(109)32(2)127-58)129-41-15-8-35(9-16-41)76(136-88-75(116)72(113)70(111)55(29-102)132-88)65(100-81(117)60(95-4)34-6-13-42(14-7-34)130-89-79(125-5)73(114)69(110)33(3)128-89)85(121)97-62(37-11-18-50(106)45(91)21-37)82(118)98-63(39)84(120)96-61-36-10-17-49(105)43(20-36)59-44(25-40(104)26-51(59)107)64(87(123)124)99-86(122)66(77)101-83(61)119/h6-26,31-33,47-48,55-58,60-77,79-80,88-90,95,102-116H,27-30,93-94H2,1-5H3,(H,96,120)(H,97,121)(H,98,118)(H,99,122)(H,100,117)(H,101,119)(H,123,124)/t31-,32-,33-,47-,48-,55+,56-,57+,58-,60-,61-,62+,63-,64?,65+,66+,67+,68+,69-,70+,71-,72-,73+,74-,75+,76+,77-,79+,80-,88+,89+,90-/m1/s1
InChI KeyZVRVZYXIMVTOQM-OAWIYRIWSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
PseudonocardiaNPAtlas
Pseudonocardia compactaLOTUS Database
Pseudonocardia compacta subsp. helvetica--
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentCyclic peptides
Alternative Parents
Substituents
  • Cyclic alpha peptide
  • Aminoglycoside core
  • Phenolic glycoside
  • O-glycosyl compound
  • Glycosyl compound
  • Disaccharide
  • Diaryl ether
  • Alpha-amino acid or derivatives
  • Phenoxy compound
  • Phenol ether
  • 2-chlorophenol
  • 2-halophenol
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Aralkylamine
  • Amino saccharide
  • Phenol
  • Halobenzene
  • Chlorobenzene
  • Benzenoid
  • Oxane
  • Monocyclic benzene moiety
  • Aryl halide
  • Aryl chloride
  • Cyclic carboximidic acid
  • Amino acid
  • Secondary alcohol
  • Amino acid or derivatives
  • 1,2-aminoalcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Secondary amine
  • Polyol
  • Monocarboxylic acid or derivatives
  • Ether
  • Secondary aliphatic amine
  • Dialkyl ether
  • Carboxylic acid
  • Carboximidic acid derivative
  • Carboximidic acid
  • Acetal
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organochloride
  • Organohalogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic 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
logP0.81ALOGPS
logP-5.6ChemAxon
logS-3.7ALOGPS
pKa (Strongest Acidic)2.98ChemAxon
pKa (Strongest Basic)9.94ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count37ChemAxon
Hydrogen Donor Count25ChemAxon
Polar Surface Area699.41 ŲChemAxon
Rotatable Bond Count19ChemAxon
Refractivity462.91 m³·mol⁻¹ChemAxon
Polarizability196.35 ųChemAxon
Number of Rings15ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA020677
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00017076
Chemspider ID78442925
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound139588919
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Takeuchi M, Takahashi S, Inukai M, Nakamura T, Kinoshita T: Helvecardins A and B, novel glycopeptide antibiotics. II. Structural elucidation. J Antibiot (Tokyo). 1991 Mar;44(3):271-7. doi: 10.7164/antibiotics.44.271. [PubMed:2026551 ]
  2. Takeuchi M, Enokita R, Okazaki T, Kagasaki T, Inukai M: Helvecardins A and B, novel glycopeptide antibiotics. I. Taxonomy, fermentation, isolation and physico-chemical properties. J Antibiot (Tokyo). 1991 Mar;44(3):263-70. doi: 10.7164/antibiotics.44.263. [PubMed:2026550 ]