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Record Information
Version2.0
Created at2020-12-09 03:49:57 UTC
Updated at2021-07-15 16:56:09 UTC
NP-MRD IDNP0006917
Secondary Accession NumbersNone
Natural Product Identification
Common NameZorbamycin
Provided ByNPAtlasNPAtlas Logo
DescriptionZorbamycin belongs to the class of organic compounds known as hybrid glycopeptides. Hybrid glycopeptides are compounds containing a carbohydrate component linked to a hybrid peptide component. Zorbamycin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Zorbamycin is found in Streptomyces and Streptomyces flavoviridis. Zorbamycin was first documented in 2007 (PMID: 17311457). Based on a literature review very few articles have been published on zorbamycin (PMID: 21210656).
Structure
Thumb
SynonymsNot Available
Chemical FormulaC55H85N19O21S2
Average Mass1412.5200 Da
Monoisotopic Mass1411.56088 Da
IUPAC Name(2R,3S,4S,5R,6R)-2-{[(2R,3S,4S,5S,6S)-2-[(1R,2S)-2-({6-amino-2-[(1S)-1-{[(2S)-2-amino-2-carbamoylethyl]amino}-2-carbamoylethyl]-5-methylpyrimidin-4-yl}formamido)-2-{[(1S,2S,3R)-1-{[(1S)-1-({2-[(4R)-4-{4-[(2-carbamimidoylethyl)carbamoyl]-1,3-thiazol-2-yl}-4,5-dihydro-1,3-thiazol-2-yl]ethyl}carbamoyl)-2-hydroxy-2-methylpropyl]carbamoyl}-2,5-dihydroxy-1-methylpentan-3-yl]carbamoyl}-1-(1H-imidazol-5-yl)ethoxy]-4,5-dihydroxy-6-methyloxan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl carbamate
Traditional Name(2R,3S,4S,5R,6R)-2-{[(2R,3S,4S,5S,6S)-2-[(1R,2S)-2-({6-amino-2-[(1S)-1-{[(2S)-2-amino-2-carbamoylethyl]amino}-2-carbamoylethyl]-5-methylpyrimidin-4-yl}formamido)-2-{[(1S,2S,3R)-1-{[(1S)-1-({2-[(4R)-4-{4-[(2-carbamimidoylethyl)carbamoyl]-1,3-thiazol-2-yl}-4,5-dihydro-1,3-thiazol-2-yl]ethyl}carbamoyl)-2-hydroxy-2-methylpropyl]carbamoyl}-2,5-dihydroxy-1-methylpentan-3-yl]carbamoyl}-1-(3H-imidazol-4-yl)ethoxy]-4,5-dihydroxy-6-methyloxan-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl carbamate
CAS Registry NumberNot Available
SMILES
C[C@@H]([C@H](O)[C@@H](CCO)NC(=O)[C@@H](NC(=O)C1=C(C)C(N)=NC(=N1)[C@H](CC(N)=O)NC[C@H](N)C(N)=O)[C@@H](O[C@@H]1O[C@@H](C)[C@@H](O)[C@H](O)[C@@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](OC(N)=O)[C@@H]1O)C1=CN=CN1)C(=O)N[C@H](C(=O)NCCC1=N[C@H](CS1)C1=NC(=CS1)C(=O)NCCC(N)=N)C(C)(C)O
InChI Identifier
InChI=1S/C55H85N19O21S2/c1-19-32(71-45(74-43(19)60)24(12-30(59)77)66-13-22(56)44(61)83)48(86)72-33(39(25-14-63-18-67-25)93-53-41(37(81)35(79)21(3)91-53)94-52-38(82)40(95-54(62)89)36(80)28(15-76)92-52)49(87)69-23(8-11-75)34(78)20(2)46(84)73-42(55(4,5)90)50(88)65-10-7-31-68-27(17-96-31)51-70-26(16-97-51)47(85)64-9-6-29(57)58/h14,16,18,20-24,27-28,33-42,52-53,66,75-76,78-82,90H,6-13,15,17,56H2,1-5H3,(H3,57,58)(H2,59,77)(H2,61,83)(H2,62,89)(H,63,67)(H,64,85)(H,65,88)(H,69,87)(H,72,86)(H,73,84)(H2,60,71,74)/t20-,21-,22-,23+,24-,27+,28+,33-,34-,35+,36+,37-,38-,39-,40-,41-,42+,52+,53-/m0/s1
InChI KeyUJKRUPHWCPAJIL-CPLCKGKLSA-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
StreptomycesNPAtlas
Streptomyces pilosusLOTUS Database
Species Where Detected
Species NameSourceReference
Streptomyces flavoviridis ATCC 21892KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hybrid glycopeptides. Hybrid glycopeptides are compounds containing a carbohydrate component linked to a hybrid peptide component.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassPeptidomimetics
Sub ClassHybrid peptides
Direct ParentHybrid glycopeptides
Alternative Parents
Substituents
  • Hybrid glycopeptide
  • Histidine or derivatives
  • Fatty acyl glycoside
  • Fatty acyl glycoside of mono- or disaccharide
  • N-acyl-alpha amino acid or derivatives
  • Valine or derivatives
  • Alpha-amino acid amide
  • Gamma amino acid or derivatives
  • Alkyl glycoside
  • O-glycosyl compound
  • Glycosyl compound
  • Beta amino acid or derivatives
  • Disaccharide
  • Alpha-amino acid or derivatives
  • N-substituted-alpha-amino acid
  • Pyrimidine-6-carboxylic acid or derivatives
  • Thiazolecarboxylic acid or derivatives
  • 2-heteroaryl carboxamide
  • Thiazolecarboxamide
  • 2,4-disubstituted 1,3-thiazole
  • Aminopyrimidine
  • Aralkylamine
  • Fatty acyl
  • Oxane
  • Fatty amide
  • N-acyl-amine
  • Pyrimidine
  • Imidolactam
  • Azole
  • Heteroaromatic compound
  • Carbamic acid ester
  • Thiazole
  • Meta-thiazoline
  • Imidazole
  • Tertiary alcohol
  • Primary carboxylic acid amide
  • Amino acid or derivatives
  • Secondary alcohol
  • Carbonic acid derivative
  • Secondary carboxylic acid amide
  • Carboxamide group
  • Acetal
  • Amidine
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Carboxylic acid amidine
  • Propargyl-type 1,3-dipolar organic compound
  • Carboxylic acid derivative
  • Secondary aliphatic amine
  • Carboximidamide
  • Secondary amine
  • Organic oxide
  • Organopnictogen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Amine
  • Alcohol
  • Organic oxygen compound
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
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
logP-1.6ALOGPS
logP-12ChemAxon
logS-4.2ALOGPS
pKa (Strongest Acidic)11.38ChemAxon
pKa (Strongest Basic)12.89ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count30ChemAxon
Hydrogen Donor Count22ChemAxon
Polar Surface Area676.41 ŲChemAxon
Rotatable Bond Count36ChemAxon
Refractivity345.66 m³·mol⁻¹ChemAxon
Polarizability138.38 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA008777
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00040733
Chemspider ID34991486
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound70697970
PDB IDNot Available
ChEBI ID67811
Good Scents IDNot Available
References
General References
  1. Wang L, Yun BS, George NP, Wendt-Pienkowski E, Galm U, Oh TJ, Coughlin JM, Zhang G, Tao M, Shen B: Glycopeptide antitumor antibiotic zorbamycin from Streptomyces flavoviridis ATCC 21892: strain improvement and structure elucidation. J Nat Prod. 2007 Mar;70(3):402-6. doi: 10.1021/np060592k. Epub 2007 Feb 21. [PubMed:17311457 ]
  2. Galm U, Wendt-Pienkowski E, Wang L, Huang SX, Unsin C, Tao M, Coughlin JM, Shen B: Comparative analysis of the biosynthetic gene clusters and pathways for three structurally related antitumor antibiotics: bleomycin, tallysomycin, and zorbamycin. J Nat Prod. 2011 Mar 25;74(3):526-36. doi: 10.1021/np1008152. Epub 2011 Jan 6. [PubMed:21210656 ]