MiMeDB: Showing metabocard for Dapdiamide E (MMDBc0007542)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 00:41:36 UTC

Update Date

2025-10-07 16:05:21 UTC

Metabolite ID

MMDBc0007542

Metabolite Identification

Common Name

Dapdiamide E

Description

Dapdiamide E is a peptide antibiotic belonging to the class of cyclic lipopeptides. It is characterized by its unique biosynthetic origin, which has been identified in specific genetic regions, notably between integrative conjugative elements (ICE) and on plasmid pPag2. The discovery of dapdiamide E's biosynthesis highlights its potential significance in microbial ecology and antibiotic production. Research indicates that additional gene clusters related to dapdiamide E and another antibiotic, B025670, are located in these genomic regions, suggesting a complex interplay of genetic elements contributing to antibiotic diversity (PMID:36344949 ). Furthermore, the identification of biosynthetic genes for dapdiamide E on a plasmid underscores the role of horizontal gene transfer in the dissemination of antibiotic resistance and production capabilities among bacterial populations (PMID:21789243 ). The study of dapdiamide E not only enhances our understanding of antibiotic biosynthesis but also provides insights into the evolutionary mechanisms that govern the emergence of new antimicrobial agents in response to environmental pressures.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152102412D          

 26 26  0  0  1  0            999 V2000
   -1.1908    5.8388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    5.8388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6671    3.3638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    5.4263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.9513    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4763    4.6013    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3651   -0.2382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    3.3638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    1.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1908    4.1888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3816    2.9513    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0796    0.1743    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.1263    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    4.1888    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3651   -1.0632    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    2.9513    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    2.1263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1908    3.3638    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9053    4.6013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    3.7763    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1908    5.0138    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2340    0.7577    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5587    1.1023    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  8  7  1  0  0  0  0
  9  7  1  0  0  0  0
 10  5  1  0  0  0  0
 11  8  1  0  0  0  0
 12  6  1  0  0  0  0
 13  3  1  0  0  0  0
 14  9  2  0  0  0  0
  5 15  1  1  0  0  0
 15 11  2  0  0  0  0
  6 16  1  1  0  0  0
 16 10  2  0  0  0  0
 17  9  1  0  0  0  0
 10 18  1  4  0  0  0
 11 19  1  4  0  0  0
 20 12  2  0  0  0  0
 21 12  1  0  0  0  0
 22  7  1  0  0  0  0
 22  8  1  0  0  0  0
  5 23  1  1  0  0  0
  6 24  1  1  0  0  0
 25  7  1  0  0  0  0
 26  8  1  0  0  0  0
M  END


  Mrv1652305152102412D          

 26 26  0  0  1  0            999 V2000
   -1.1908    5.8388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    5.8388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6671    3.3638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    5.4263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.9513    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4763    4.6013    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3651   -0.2382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    3.3638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    1.7138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1908    4.1888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3816    2.9513    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0796    0.1743    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    2.1263    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    4.1888    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3651   -1.0632    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    2.9513    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4763    2.1263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1908    3.3638    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9053    4.6013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743    0.1743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9526    3.7763    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1908    5.0138    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2340    0.7577    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5587    1.1023    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  8  7  1  0  0  0  0
  9  7  1  0  0  0  0
 10  5  1  0  0  0  0
 11  8  1  0  0  0  0
 12  6  1  0  0  0  0
 13  3  1  0  0  0  0
 14  9  2  0  0  0  0
  5 15  1  1  0  0  0
 15 11  2  0  0  0  0
  6 16  1  1  0  0  0
 16 10  2  0  0  0  0
 17  9  1  0  0  0  0
 10 18  1  4  0  0  0
 11 19  1  4  0  0  0
 20 12  2  0  0  0  0
 21 12  1  0  0  0  0
 22  7  1  0  0  0  0
 22  8  1  0  0  0  0
  5 23  1  1  0  0  0
  6 24  1  1  0  0  0
 25  7  1  0  0  0  0
 26  8  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0007542

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](CN)(N=C(O)C1([H])OC1([H])C(O)=N)C(O)=N[C@@]([H])(C(C)C)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H20N4O6/c1-4(2)6(12(20)21)16-10(18)5(3-13)15-11(19)8-7(22-8)9(14)17/h4-8H,3,13H2,1-2H3,(H2,14,17)(H,15,19)(H,16,18)(H,20,21)/t5-,6-,7?,8?/m0/s1

> <INCHI_KEY>
BQMJFERCSPVSGR-LHZZQDSXSA-N

> <FORMULA>
C12H20N4O6

> <MOLECULAR_WEIGHT>
316.314

> <EXACT_MASS>
316.13828438

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
30.616893920890817

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-{[(2S)-3-amino-1-hydroxy-2-({hydroxy[3-(C-hydroxycarbonimidoyl)oxiran-2-yl]methylidene}amino)propylidene]amino}-3-methylbutanoic acid

> <ALOGPS_LOGP>
-2.80

> <JCHEM_LOGP>
-5.502757350530824

> <ALOGPS_LOGS>
-3.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.590429701290282

> <JCHEM_PKA_STRONGEST_ACIDIC>
-3.6710849753497126

> <JCHEM_PKA_STRONGEST_BASIC>
12.337772483039775

> <JCHEM_POLAR_SURFACE_AREA>
185.10999999999999

> <JCHEM_REFRACTIVITY>
83.29710000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.19e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-{[(2S)-3-amino-1-hydroxy-2-({hydroxy[3-(C-hydroxycarbonimidoyl)oxiran-2-yl]methylidene}amino)propylidene]amino}-3-methylbutanoic acid

> <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      -2.223  10.899   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.445  10.899   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.112   6.279   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.889  10.129   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.778   5.509   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.889   8.589   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.215   0.325   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.445   1.659   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.548  -0.445   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.445   6.279   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.445   3.199   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.223   7.819   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       4.446   5.509   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       3.882   0.325   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       1.778   3.969   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       0.445   7.819   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0       2.548  -1.985   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -0.889   5.509   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -0.889   3.969   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -2.223   6.279   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -3.556   8.589   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -0.325   0.325   0.000  0.00  0.00           O+0
HETATM   23  H   UNK     0       1.778   7.049   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0      -2.223   9.359   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       2.304   1.414   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0      -1.043   2.058   0.000  0.00  0.00           H+0
CONECT    1    4                                                            
CONECT    2    4                                                            
CONECT    3    5   13                                                       
CONECT    4    1    2    6                                                  
CONECT    5    3   10   15   23                                             
CONECT    6    4   12   16   24                                             
CONECT    7    8    9   22   25                                             
CONECT    8    7   11   22   26                                             
CONECT    9    7   14   17                                                  
CONECT   10    5   16   18                                                  
CONECT   11    8   15   19                                                  
CONECT   12    6   20   21                                                  
CONECT   13    3                                                            
CONECT   14    9                                                            
CONECT   15    5   11                                                       
CONECT   16    6   10                                                       
CONECT   17    9                                                            
CONECT   18   10                                                            
CONECT   19   11                                                            
CONECT   20   12                                                            
CONECT   21   12                                                            
CONECT   22    7    8                                                       
CONECT   23    5                                                            
CONECT   24    6                                                            
CONECT   25    7                                                            
CONECT   26    8                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   52    0
END

Synonyms

Not Available

Molecular Formula

C₁₂H₂₀N₄O₆

Average Mass

316.314

Monoisotopic Mass

316.13828438

IUPAC Name

(2S)-2-{[(2S)-3-amino-1-hydroxy-2-({hydroxy[3-(C-hydroxycarbonimidoyl)oxiran-2-yl]methylidene}amino)propylidene]amino}-3-methylbutanoic acid

Traditional Name

(2S)-2-{[(2S)-3-amino-1-hydroxy-2-({hydroxy[3-(C-hydroxycarbonimidoyl)oxiran-2-yl]methylidene}amino)propylidene]amino}-3-methylbutanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](CN)(N=C(O)C1([H])OC1([H])C(O)=N)C(O)=N[C@@]([H])(C(C)C)C(O)=O

InChI Identifier

InChI=1S/C12H20N4O6/c1-4(2)6(12(20)21)16-10(18)5(3-13)15-11(19)8-7(22-8)9(14)17/h4-8H,3,13H2,1-2H3,(H2,14,17)(H,15,19)(H,16,18)(H,20,21)/t5-,6-,7?,8?/m0/s1

InChI Key

BQMJFERCSPVSGR-LHZZQDSXSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

Alpha-dipeptide
N-acyl-alpha amino acid or derivatives
Valine or derivatives
N-acyl-alpha-amino acid
N-acyl-l-alpha-amino acid
Alpha-amino acid amide
Beta amino acid or derivatives
N-substituted-alpha-amino acid
Alpha-amino acid or derivatives
Branched fatty acid
Heterocyclic fatty acid
Epoxy fatty acid
Methyl-branched fatty acid
Fatty acyl
Oxirane carboxylic acid or derivatives
Fatty acid
Amino acid or derivatives
Amino acid
Primary carboxylic acid amide
Secondary carboxylic acid amide
Carboxamide group
Oxacycle
Organoheterocyclic compound
Carboxylic acid
Dialkyl ether
Oxirane
Ether
Monocarboxylic acid or derivatives
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Amine
Primary amine
Organic oxide
Organooxygen compound
Primary aliphatic amine
Hydrocarbon derivative
Organonitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.32 g/L	ALOGPS
logP	-2.8	ALOGPS
logP	-5.5	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	-3.7	ChemAxon
pKa (Strongest Basic)	12.34	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	185.11 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	83.3 m³·mol⁻¹	ChemAxon
Polarizability	30.62 Å³	ChemAxon
Number of Rings	1	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

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

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	Proteobacteria	1	Human	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	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

58837247

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

45379525

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for Dapdiamide E (MMDBc0007542)

MOL for #<Metabolite:0x00007f2ac45a37f0>

3D MOL for #<Metabolite:0x00007f2ac45a37f0>

3D SDF for #<Metabolite:0x00007f2ac45a37f0>

3D-SDF for #<Metabolite:0x00007f2ac45a37f0>

PDB for #<Metabolite:0x00007f2ac45a37f0>

3D PDB for #<Metabolite:0x00007f2ac45a37f0>

SMILES for #<Metabolite:0x00007f2ac45a37f0>

INCHI for #<Metabolite:0x00007f2ac45a37f0>

Structure for #<Metabolite:0x00007f2ac45a37f0>

3D Structure for #<Metabolite:0x00007f2ac45a37f0>