MiMeDB: Showing metabocard for dapdiamide A (MMDBc0055883)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:09:45 UTC

Update Date

2022-08-12 20:09:28 UTC

Metabolite ID

MMDBc0055883

Metabolite Identification

Common Name

dapdiamide A

Description

dapdiamide A 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. dapdiamide A 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. Based on a literature review very few articles have been published on dapdiamide A.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222092D          

 25 24  0  0  1  0            999 V2000
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9500    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5375    3.5724    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7750    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    2.8579    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  6  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  5  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12 10  1  0  0  0  0
  7 13  1  6  0  0  0
 14  8  2  0  0  0  0
 15  5  1  4  0  0  0
 15  9  2  0  0  0  0
 10 16  1  1  0  0  0
 16 11  2  0  0  0  0
 17  8  1  0  0  0  0
 18  9  1  0  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  3  1  0  0  0  0
 23  4  1  0  0  0  0
  7 24  1  6  0  0  0
 10 25  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0055883

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(=C(\[H])C(O)=NC[C@]([H])(N)C(O)=N[C@@]([H])(C(C)C)C(O)=O)C(O)=N

> <INCHI_IDENTIFIER>
InChI=1S/C12H20N4O5/c1-6(2)10(12(20)21)16-11(19)7(13)5-15-9(18)4-3-8(14)17/h3-4,6-7,10H,5,13H2,1-2H3,(H2,14,17)(H,15,18)(H,16,19)(H,20,21)/b4-3+/t7-,10-/m0/s1

> <INCHI_KEY>
JAGLEOBXISHNNM-BRUQVKLWSA-N

> <FORMULA>
C12H20N4O5

> <MOLECULAR_WEIGHT>
300.315

> <EXACT_MASS>
300.14336976

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
29.848027945824374

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-{[(2S)-2-amino-1-hydroxy-3-{[(2E)-1-hydroxy-3-(C-hydroxycarbonimidoyl)prop-2-en-1-ylidene]amino}propylidene]amino}-3-methylbutanoic acid

> <JCHEM_LOGP>
-5.316133977469547

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.5796414544794164

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.2060336836900314

> <JCHEM_PKA_STRONGEST_BASIC>
12.32547676509157

> <JCHEM_POLAR_SURFACE_AREA>
172.57999999999998

> <JCHEM_REFRACTIVITY>
85.2008

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-{[(2S)-2-amino-1-hydroxy-3-{[(2E)-1-hydroxy-3-(C-hydroxycarbonimidoyl)prop-2-en-1-ylidene]amino}propylidene]amino}-3-methylbutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.080  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.470   4.001   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.240   5.335   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.160   2.667   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -2.667   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       1.540   2.667   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       8.470   6.668   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       4.620   2.667   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      10.780   5.335   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       6.930   1.334   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.540  -2.667   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -0.770  -4.001   0.000  0.00  0.00           O+0
HETATM   22  H   UNK     0       9.240   2.667   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       6.160   5.335   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       3.080  -0.000   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0      -1.540  -2.667   0.000  0.00  0.00           H+0
CONECT    1    6                                                            
CONECT    2    6                                                            
CONECT    3    4    8   22                                                  
CONECT    4    3    9   23                                                  
CONECT    5    7   15                                                       
CONECT    6    1    2   10                                                  
CONECT    7    5   11   13   24                                             
CONECT    8    3   14   17                                                  
CONECT    9    4   15   18                                                  
CONECT   10    6   12   16   25                                             
CONECT   11    7   16   19                                                  
CONECT   12   10   20   21                                                  
CONECT   13    7                                                            
CONECT   14    8                                                            
CONECT   15    5    9                                                       
CONECT   16   10   11                                                       
CONECT   17    8                                                            
CONECT   18    9                                                            
CONECT   19   11                                                            
CONECT   20   12                                                            
CONECT   21   12                                                            
CONECT   22    3                                                            
CONECT   23    4                                                            
CONECT   24    7                                                            
CONECT   25   10                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   48    0
END

Synonyms

Not Available

Molecular Formula

C₁₂H₂₀N₄O₅

Average Mass

300.315

Monoisotopic Mass

300.14336976

IUPAC Name

(2S)-2-{[(2S)-2-amino-1-hydroxy-3-{[(2E)-1-hydroxy-3-(C-hydroxycarbonimidoyl)prop-2-en-1-ylidene]amino}propylidene]amino}-3-methylbutanoic acid

Traditional Name

(2S)-2-{[(2S)-2-amino-1-hydroxy-3-{[(2E)-1-hydroxy-3-(C-hydroxycarbonimidoyl)prop-2-en-1-ylidene]amino}propylidene]amino}-3-methylbutanoic acid

CAS Registry Number

Not Available

SMILES

[H]\C(=C(\[H])C(O)=NC[C@]([H])(N)C(O)=N[C@@]([H])(C(C)C)C(O)=O)C(O)=N

InChI Identifier

InChI=1S/C12H20N4O5/c1-6(2)10(12(20)21)16-11(19)7(13)5-15-9(18)4-3-8(14)17/h3-4,6-7,10H,5,13H2,1-2H3,(H2,14,17)(H,15,18)(H,16,19)(H,20,21)/b4-3+/t7-,10-/m0/s1

InChI Key

JAGLEOBXISHNNM-BRUQVKLWSA-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
Valine or derivatives
N-acyl-alpha amino acid or derivatives
N-acyl-l-alpha-amino acid
Alpha-amino acid amide
Beta amino acid or derivatives
Alpha-amino acid or derivatives
Branched fatty acid
Methyl-branched fatty acid
N-acyl-amine
Fatty acyl
Primary carboxylic acid amide
Carboxamide group
Amino acid
Secondary carboxylic acid amide
Amino acid or derivatives
Carboxylic acid
Monocarboxylic acid or derivatives
Organic nitrogen compound
Organonitrogen compound
Primary aliphatic amine
Organooxygen compound
Primary amine
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Amine
Organic oxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

enamide (CHEBI:85330 )
dapdiamide (CHEBI:85330 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-5.3	ChemAxon
pKa (Strongest Acidic)	0.21	ChemAxon
pKa (Strongest Basic)	12.33	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	172.58 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	85.2 m³·mol⁻¹	ChemAxon
Polarizability	29.85 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_5) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum

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

Metabolic Reactions

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

Exposure Sources

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

34999419

KEGG Compound ID

Not Available

BioCyc ID

CPD-17539

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

45380223

PDB ID

Not Available

ChEBI ID

84320

Food Biomarker Ontology

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 A (MMDBc0055883)

MOL for #<Metabolite:0x00007fdb58337f58>

3D MOL for #<Metabolite:0x00007fdb58337f58>

3D SDF for #<Metabolite:0x00007fdb58337f58>

3D-SDF for #<Metabolite:0x00007fdb58337f58>

PDB for #<Metabolite:0x00007fdb58337f58>

3D PDB for #<Metabolite:0x00007fdb58337f58>

SMILES for #<Metabolite:0x00007fdb58337f58>

INCHI for #<Metabolite:0x00007fdb58337f58>

Structure for #<Metabolite:0x00007fdb58337f58>

3D Structure for #<Metabolite:0x00007fdb58337f58>