Showing metabocard for Lugdunin (MMDBc0024559)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-05-15 14:21:35 UTC
Update Date2022-08-31 06:49:44 UTC
Metabolite IDMMDBc0024559
Metabolite Identification
Common NameLugdunin
Descriptionlugdunin belongs to the class of organic compounds known as cyclic peptides. Cyclic peptides are compounds containing a cyclic moiety bearing a peptide backbone. lugdunin is a very strong basic compound (based on its pKa). It was isolated in 2016 after Staphylococcus lugdunensis was identified as the species of bacteria from the human nose that suppressed growth of species of disease-causing bacteria in that part of the human microbiome.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00005634c2a3d0c0>


  Mrv1652305152116212D          

 63 66  0  0  1  0            999 V2000
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    4.8308   -4.4402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for #<Metabolite:0x00005634c2a3d0c0>

Download
3D SDF for #<Metabolite:0x00005634c2a3d0c0>

  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

$$$$

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3D-SDF for #<Metabolite:0x00005634c2a3d0c0>
Download
PDB for #<Metabolite:0x00005634c2a3d0c0>
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

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3D PDB for #<Metabolite:0x00005634c2a3d0c0>
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SMILES for #<Metabolite:0x00005634c2a3d0c0>
[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
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INCHI for #<Metabolite:0x00005634c2a3d0c0>
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
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SynonymsNot Available
Molecular FormulaC40H62N8O6S
Average Mass783.05
Monoisotopic Mass782.451302922
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 NumberNot 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 KeyQZNGYMKAHFFKCJ-ZBQZSICZSA-N