MiMeDB: Showing metabocard for Lynamicin D (MMDBc0019836)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 09:51:02 UTC

Update Date

2025-10-07 16:07:01 UTC

Metabolite ID

MMDBc0019836

Metabolite Identification

Common Name

Lynamicin D

Description

Lynamicin D is a member of the chemical class of bisindole alkaloids. Its chemical structure features a unique pyrrole moiety, which is integral to its biological activity. This compound has been the subject of various synthetic efforts, including a biomimetic approach that seeks to replicate its natural synthesis pathway, as detailed in studies exploring its complex alkaloid framework (PMID:38450726 , PMID:34377425 ). Lynamicin D exhibits antimicrobial properties and has been shown to influence splicing mechanisms by inducing the expression of SR protein kinase 1 (SRPK1), a key regulator in both constitutive and alternative splicing of pre-mRNAs (PMID:28139279 ). Additionally, it has been evaluated for its interaction with multiple drug target enzymes, demonstrating potent inhibitory effects on Topoisomerase II, Cathepsin K, and various cytochrome P450 enzymes, among others (PMID:25205496 ). The total synthesis of lynamicin D has been successfully achieved using a Suzuki coupling method, highlighting its significance in synthetic organic chemistry (PMID:28139279 ). Overall, lynamicin D serves as an intriguing example of how complex natural products can be synthesized and studied for their multifaceted biological roles.

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004261501102D          

 33 37  0  0  0  0            999 V2000
    3.4312   -2.1030    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6062   -2.1030    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -2.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6062   -3.5319    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687   -2.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -3.4849    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -3.2299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3220   -3.3793    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -4.5353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2716   -4.8709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -2.4049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.9200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3529   -2.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8378   -1.5075    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3529   -0.8401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5244   -0.0331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9113    0.5189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1267    0.2640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4864    0.8160    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0448   -0.5430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668   -1.5229    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  7 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 13 22  1  0  0  0  0
 16 22  1  0  0  0  0
 12 23  1  0  0  0  0
  5 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 32 33  2  0  0  0  0
 24 33  1  0  0  0  0
 27 33  1  0  0  0  0
M  END


  Mrv1533004261501102D          

 33 37  0  0  0  0            999 V2000
    3.4312   -2.1030    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6062   -2.1030    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -2.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6062   -3.5319    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687   -2.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -3.4849    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -3.2299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3220   -3.3793    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -4.5353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2716   -4.8709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -2.4049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.9200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3529   -2.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8378   -1.5075    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3529   -0.8401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5244   -0.0331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9113    0.5189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1267    0.2640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4864    0.8160    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0448   -0.5430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668   -1.5229    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  7 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 13 22  1  0  0  0  0
 16 22  1  0  0  0  0
 12 23  1  0  0  0  0
  5 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 32 33  2  0  0  0  0
 24 33  1  0  0  0  0
 27 33  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0019836

> <DATABASE_NAME>
MIME

> <SMILES>
COC(=O)C1=C(C2=CNC3=CC=C(Cl)C=C23)C(=C(N1)C(=O)OC)C1=CNC2=CC=C(Cl)C=C12

> <INCHI_IDENTIFIER>
InChI=1S/C24H17Cl2N3O4/c1-32-23(30)21-19(15-9-27-17-5-3-11(25)7-13(15)17)20(22(29-21)24(31)33-2)16-10-28-18-6-4-12(26)8-14(16)18/h3-10,27-29H,1-2H3

> <INCHI_KEY>
YYBKJQDTRQASSS-UHFFFAOYSA-N

> <FORMULA>
C24H17Cl2N3O4

> <MOLECULAR_WEIGHT>
482.32

> <EXACT_MASS>
481.0596114

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
47.18118969250969

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,5-dimethyl 3,4-bis(5-chloro-1H-indol-3-yl)-1H-pyrrole-2,5-dicarboxylate

> <ALOGPS_LOGP>
5.09

> <JCHEM_LOGP>
5.6001501666666655

> <ALOGPS_LOGS>
-6.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.120905546449286

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.206934080204427

> <JCHEM_PKA_STRONGEST_BASIC>
-6.838668855370437

> <JCHEM_POLAR_SURFACE_AREA>
99.97

> <JCHEM_REFRACTIVITY>
126.67739999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.70e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
lynamicin D

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-APR-15         0                                  
HETATM    1  C   UNK     0       6.405  -3.926   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       4.865  -3.926   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.095  -5.259   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.865  -6.593   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.555  -5.259   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.650  -6.505   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.185  -6.029   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.061  -6.934   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.468  -6.308   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -0.900  -8.466   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.507  -9.092   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.185  -4.489   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.061  -3.584   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.525  -4.060   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -3.431  -2.814   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      -2.525  -1.568   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.846  -0.062   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.701   0.969   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.237   0.493   0.000  0.00  0.00           C+0
HETATM   20 Cl   UNK     0       0.908   1.523   0.000  0.00  0.00          Cl+0
HETATM   21  C   UNK     0       0.084  -1.014   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.061  -2.044   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   31 Cl   UNK     0       7.591  -2.843   0.000  0.00  0.00          Cl+0
HETATM   32  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   23                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10                                                            
CONECT   12    7   13   23                                                  
CONECT   13   12   14   22                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   22                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   13   16                                                  
CONECT   23   12    5   24                                                  
CONECT   24   23   25   33                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   33                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   24   27                                                  
MASTER        0    0    0    0    0    0    0    0   33    0   74    0
END

Synonyms

Not Available

Molecular Formula

C₂₄H₁₇Cl₂N₃O₄

Average Mass

482.32

Monoisotopic Mass

481.0596114

IUPAC Name

2,5-dimethyl 3,4-bis(5-chloro-1H-indol-3-yl)-1H-pyrrole-2,5-dicarboxylate

Traditional Name

lynamicin D

CAS Registry Number

Not Available

SMILES

COC(=O)C1=C(C2=CNC3=CC=C(Cl)C=C23)C(=C(N1)C(=O)OC)C1=CNC2=CC=C(Cl)C=C12

InChI Identifier

InChI=1S/C24H17Cl2N3O4/c1-32-23(30)21-19(15-9-27-17-5-3-11(25)7-13(15)17)20(22(29-21)24(31)33-2)16-10-28-18-6-4-12(26)8-14(16)18/h3-10,27-29H,1-2H3

InChI Key

YYBKJQDTRQASSS-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

Indoles

Alternative Parents

Substituents

Indole
Pyrrole-2-carboxylic acid or derivatives
Aryl chloride
Aryl halide
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Methyl ester
Carboxylic acid ester
Carboxylic acid derivative
Azacycle
Organooxygen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Organic nitrogen compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
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	0.00037 g/L	ALOGPS
logP	5.09	ALOGPS
logP	5.6	ChemAxon
logS	-6.1	ALOGPS
pKa (Strongest Acidic)	7.21	ChemAxon
pKa (Strongest Basic)	-6.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	99.97 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	126.68 m³·mol⁻¹	ChemAxon
Polarizability	47.18 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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	Actinobacteria	1	Human ; Human feces; Human saliva; Human urine; Human supragingival plaque; Human sputum; Human subgingival plaque	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11329151

PDB ID

Not Available

ChEBI ID

Not Available

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 Lynamicin D (MMDBc0019836)

MOL for #<Metabolite:0x00007f8dc16312e8>

3D MOL for #<Metabolite:0x00007f8dc16312e8>

3D SDF for #<Metabolite:0x00007f8dc16312e8>

3D-SDF for #<Metabolite:0x00007f8dc16312e8>

PDB for #<Metabolite:0x00007f8dc16312e8>

3D PDB for #<Metabolite:0x00007f8dc16312e8>

SMILES for #<Metabolite:0x00007f8dc16312e8>

INCHI for #<Metabolite:0x00007f8dc16312e8>

Structure for #<Metabolite:0x00007f8dc16312e8>

3D Structure for #<Metabolite:0x00007f8dc16312e8>