MiMeDB: Showing metabocard for Lugdunin (MMDBc0024559)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 14:21:35 UTC

Update Date

2025-10-07 16:07:27 UTC

Metabolite ID

MMDBc0024559

Metabolite Identification

Common Name

Lugdunin

Description

Lugdunin is a thiazolidine-containing antimicrobial peptide classified as a natural product in the chemical class of peptides. It is produced by the bacterium Staphylococcus lugdunensis, which has gained attention due to its emerging role as a coagulase-negative Staphylococcus (CoNS) pathogen. The chemical structure of lugdunin allows it to exhibit antibacterial activity primarily against gram-positive bacteria, as evidenced by studies that evaluated its effects under various conditions. Specifically, optimal conditions for lugdunin activity were identified at pH 7.5 with a 72-hour incubation period, leading to antimicrobial effects against several strains, including Staphylococcus aureus and Enterococcus faecium (PMID:40986964 ). In addition to its antibacterial properties, the study revealed distinct susceptibility phenotypes among lugdunin-nonproducing S. lugdunensis strains, highlighting the complexity of its interactions within microbial communities (PMID:40986964 ). Further research has also explored multi-cationic derivatives of lugdunin, expanding its antimicrobial spectrum to include both gram-positive and gram-negative bacteria (PMID:40848518 ). Overall, lugdunin represents a significant chemical entity with potential applications in combating antibiotic-resistant infections.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152116212D          

 63 66  0  0  1  0            999 V2000
    5.5426   -3.2011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8308   -4.4402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.2950   -0.3709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.7065   -6.7882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 63 40  1  0  0  0  0
M  END


  Mrv1652305152116212D          

 63 66  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
MMDBc0024559

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12CSC([H])(N1)[C@@]([H])(N=C(O)[C@]([H])(N=C(O)[C@@]([H])(N=C(O)[C@@]([H])(CC(C)C)N=C(O)[C@]([H])(CC1=CNC3=CC=CC=C13)N=C(O)[C@]([H])(N=C2O)C(C)C)C(C)C)C(C)C)C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C40H62N8O6S/c1-19(2)15-27-35(50)45-31(21(5)6)38(53)47-32(22(7)8)39(54)48-33(23(9)10)40-44-29(18-55-40)36(51)46-30(20(3)4)37(52)43-28(34(49)42-27)16-24-17-41-26-14-12-11-13-25(24)26/h11-14,17,19-23,27-33,40-41,44H,15-16,18H2,1-10H3,(H,42,49)(H,43,52)(H,45,50)(H,46,51)(H,47,53)(H,48,54)/t27-,28+,29+,30-,31+,32-,33+,40?/m1/s1

> <INCHI_KEY>
QZNGYMKAHFFKCJ-ZBQZSICZSA-N

> <FORMULA>
C40H62N8O6S

> <MOLECULAR_WEIGHT>
783.05

> <EXACT_MASS>
782.451302922

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
117

> <JCHEM_AVERAGE_POLARIZABILITY>
85.42352793791031

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,4R,7S,10R,13S,16R,19S)-7-[(1H-indol-3-yl)methyl]-10-(2-methylpropyl)-4,13,16,19-tetrakis(propan-2-yl)-21-thia-3,6,9,12,15,18,23-heptaazabicyclo[18.2.1]tricosa-2,5,8,11,14,17-hexaene-2,5,8,11,14,17-hexol

> <ALOGPS_LOGP>
3.58

> <JCHEM_LOGP>
6.143849446887268

> <ALOGPS_LOGS>
-4.73

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.563773409415031

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4389790164341179

> <JCHEM_PKA_STRONGEST_BASIC>
5.768631898344186

> <JCHEM_POLAR_SURFACE_AREA>
223.35999999999996

> <JCHEM_REFRACTIVITY>
214.80620000000008

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.45e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,4R,7S,10R,13S,16R,19S)-7-(1H-indol-3-ylmethyl)-4,13,16,19-tetraisopropyl-10-(2-methylpropyl)-21-thia-3,6,9,12,15,18,23-heptaazabicyclo[18.2.1]tricosa-2,5,8,11,14,17-hexaene-2,5,8,11,14,17-hexol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      10.346  -5.975   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.018  -8.288   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.502  -2.511   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.551  -0.692   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.888 -10.186   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.919 -12.671   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.982 -14.726   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.529 -13.934   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.119 -12.863   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.326 -11.365   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.909   2.736   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.446   2.832   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.223   1.357   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.297   1.548   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.679  -5.981   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.258  -1.983   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.990  -2.243   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -4.066  -6.751   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.014  -6.748   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.001  -2.165   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.686 -11.149   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.027 -13.595   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -2.791 -11.477   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.690  -1.417   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.074   0.074   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.611   0.170   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.347  -6.754   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.031  -3.506   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.603  -6.271   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.049  -3.291   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.251 -10.589   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       1.569 -12.124   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -1.926 -10.202   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       5.238  -4.464   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.350  -8.294   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -1.938  -4.883   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       1.549  -2.946   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       4.049 -11.552   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       0.067 -11.785   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -2.597  -8.816   0.000  0.00  0.00           C+0
HETATM   41  N   UNK     0       8.177  -1.263   0.000  0.00  0.00           N+0
HETATM   42  N   UNK     0       5.011  -5.987   0.000  0.00  0.00           N+0
HETATM   43  N   UNK     0       2.599  -4.072   0.000  0.00  0.00           N+0
HETATM   44  N   UNK     0      -1.732  -7.542   0.000  0.00  0.00           N+0
HETATM   45  N   UNK     0       5.018  -9.067   0.000  0.00  0.00           N+0
HETATM   46  N   UNK     0      -0.402  -4.764   0.000  0.00  0.00           N+0
HETATM   47  N   UNK     0       2.614 -10.993   0.000  0.00  0.00           N+0
HETATM   48  N   UNK     0      -0.390 -10.314   0.000  0.00  0.00           N+0
HETATM   49  O   UNK     0       6.670  -3.898   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0       7.686  -9.061   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      -2.808  -3.612   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       2.000  -1.473   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       4.282 -13.075   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      -0.978 -12.916   0.000  0.00  0.00           O+0
HETATM   55  S   UNK     0      -4.063  -8.291   0.000  0.00  0.00           S+0
HETATM   56  H   UNK     0       7.682  -7.521   0.000  0.00  0.00           H+0
HETATM   57  H   UNK     0       2.825  -2.549   0.000  0.00  0.00           H+0
HETATM   58  H   UNK     0      -1.067  -6.153   0.000  0.00  0.00           H+0
HETATM   59  H   UNK     0      -1.452  -3.637   0.000  0.00  0.00           H+0
HETATM   60  H   UNK     0       6.453  -9.627   0.000  0.00  0.00           H+0
HETATM   61  H   UNK     0       3.072 -12.463   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0      -1.255 -11.588   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0      -3.626  -9.962   0.000  0.00  0.00           H+0
CONECT    1   19                                                            
CONECT    2   19                                                            
CONECT    3   20                                                            
CONECT    4   20                                                            
CONECT    5   21                                                            
CONECT    6   21                                                            
CONECT    7   22                                                            
CONECT    8   22                                                            
CONECT    9   23                                                            
CONECT   10   23                                                            
CONECT   11   12   13                                                       
CONECT   12   11   14                                                       
CONECT   13   11   25                                                       
CONECT   14   12   26                                                       
CONECT   15   19   27                                                       
CONECT   16   24   28                                                       
CONECT   17   24   41                                                       
CONECT   18   29   55                                                       
CONECT   19    1    2   15                                                  
CONECT   20    3    4   30                                                  
CONECT   21    5    6   31                                                  
CONECT   22    7    8   32                                                  
CONECT   23    9   10   33                                                  
CONECT   24   16   17   25                                                  
CONECT   25   13   24   26                                                  
CONECT   26   14   25   41                                                  
CONECT   27   15   35   42   56                                             
CONECT   28   16   34   43   57                                             
CONECT   29   18   36   44   58                                             
CONECT   30   20   37   46   59                                             
CONECT   31   21   38   45   60                                             
CONECT   32   22   39   47   61                                             
CONECT   33   23   40   48   62                                             
CONECT   34   28   42   49                                                  
CONECT   35   27   45   50                                                  
CONECT   36   29   46   51                                                  
CONECT   37   30   43   52                                                  
CONECT   38   31   47   53                                                  
CONECT   39   32   48   54                                                  
CONECT   40   33   44   55   63                                             
CONECT   41   17   26                                                       
CONECT   42   27   34                                                       
CONECT   43   28   37                                                       
CONECT   44   29   40                                                       
CONECT   45   31   35                                                       
CONECT   46   30   36                                                       
CONECT   47   32   38                                                       
CONECT   48   33   39                                                       
CONECT   49   34                                                            
CONECT   50   35                                                            
CONECT   51   36                                                            
CONECT   52   37                                                            
CONECT   53   38                                                            
CONECT   54   39                                                            
CONECT   55   18   40                                                       
CONECT   56   27                                                            
CONECT   57   28                                                            
CONECT   58   29                                                            
CONECT   59   30                                                            
CONECT   60   31                                                            
CONECT   61   32                                                            
CONECT   62   33                                                            
CONECT   63   40                                                            
MASTER        0    0    0    0    0    0    0    0   63    0  132    0
END

Synonyms

Not Available

Molecular Formula

C₄₀H₆₂N₈O₆S

Average Mass

783.05

Monoisotopic Mass

782.451302922

IUPAC Name

(1R,4R,7S,10R,13S,16R,19S)-7-[(1H-indol-3-yl)methyl]-10-(2-methylpropyl)-4,13,16,19-tetrakis(propan-2-yl)-21-thia-3,6,9,12,15,18,23-heptaazabicyclo[18.2.1]tricosa-2,5,8,11,14,17-hexaene-2,5,8,11,14,17-hexol

Traditional Name

(1R,4R,7S,10R,13S,16R,19S)-7-(1H-indol-3-ylmethyl)-4,13,16,19-tetraisopropyl-10-(2-methylpropyl)-21-thia-3,6,9,12,15,18,23-heptaazabicyclo[18.2.1]tricosa-2,5,8,11,14,17-hexaene-2,5,8,11,14,17-hexol

CAS Registry Number

Not Available

SMILES

[H][C@@]12CSC([H])(N1)[C@@]([H])(N=C(O)[C@]([H])(N=C(O)[C@@]([H])(N=C(O)[C@@]([H])(CC(C)C)N=C(O)[C@]([H])(CC1=CNC3=CC=CC=C13)N=C(O)[C@]([H])(N=C2O)C(C)C)C(C)C)C(C)C)C(C)C

InChI Identifier

InChI=1S/C40H62N8O6S/c1-19(2)15-27-35(50)45-31(21(5)6)38(53)47-32(22(7)8)39(54)48-33(23(9)10)40-44-29(18-55-40)36(51)46-30(20(3)4)37(52)43-28(34(49)42-27)16-24-17-41-26-14-12-11-13-25(24)26/h11-14,17,19-23,27-33,40-41,44H,15-16,18H2,1-10H3,(H,42,49)(H,43,52)(H,45,50)(H,46,51)(H,47,53)(H,48,54)/t27-,28+,29+,30-,31+,32-,33+,40?/m1/s1

InChI Key

QZNGYMKAHFFKCJ-ZBQZSICZSA-N

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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Cyclic peptides

Alternative Parents

Substituents

Cyclic alpha peptide
3-alkylindole
Indole
Indole or derivatives
Substituted pyrrole
Benzenoid
Pyrrole
Heteroaromatic compound
Thiazolidine
Cyclic carboximidic acid
Secondary aliphatic amine
Polyol
Secondary amine
Azacycle
Organoheterocyclic compound
Thioether
Hemithioaminal
Dialkylthioether
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organic nitrogen compound
Amine
Organic oxygen compound
Organopnictogen compound
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.014 g/L	ALOGPS
logP	3.58	ALOGPS
logP	6.14	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	1.44	ChemAxon
pKa (Strongest Basic)	5.77	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	223.36 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	214.81 m³·mol⁻¹	ChemAxon
Polarizability	85.42 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Firmicutes	1	Human	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

57427231

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Lugdunin

METLIN ID

Not Available

PubChem Compound

121596231

PDB ID

Not Available

ChEBI ID

133127

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Lugdunin (MMDBc0024559)

MOL for #<Metabolite:0x00007f8dc4722aa0>

3D MOL for #<Metabolite:0x00007f8dc4722aa0>

3D SDF for #<Metabolite:0x00007f8dc4722aa0>

3D-SDF for #<Metabolite:0x00007f8dc4722aa0>

PDB for #<Metabolite:0x00007f8dc4722aa0>

3D PDB for #<Metabolite:0x00007f8dc4722aa0>

SMILES for #<Metabolite:0x00007f8dc4722aa0>

INCHI for #<Metabolite:0x00007f8dc4722aa0>

Structure for #<Metabolite:0x00007f8dc4722aa0>

3D Structure for #<Metabolite:0x00007f8dc4722aa0>