MiMeDB: Showing metabocard for Dapdiamide B (MMDBc0009501)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 02:00:27 UTC

Update Date

2025-10-07 16:05:37 UTC

Metabolite ID

MMDBc0009501

Metabolite Identification

Common Name

Dapdiamide B

Description

Dapdiamide B is a secondary metabolite belonging to the class of peptides. There is limited literature available on Dapdiamide B, indicating that further research is needed to fully understand its properties and potential biological significance.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152104002D          

 27 26  0  0  1  0            999 V2000
    0.5230   -0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    6.0770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    5.6645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    3.6020    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
    2.6664    3.1895    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8099    6.9020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    4.8395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6664    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    3.6020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    7.3145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    4.4270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5243    7.3145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    4.4270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5243    5.6645    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    6.0770    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    2.7770    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  5  4  2  0  0  0  0
  7  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  6  1  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  1  0  0  0  0
 13 11  1  0  0  0  0
  8 14  1  6  0  0  0
 15  9  2  0  0  0  0
 16  6  1  4  0  0  0
 16 10  2  0  0  0  0
 11 17  1  1  0  0  0
 17 12  2  0  0  0  0
 18  9  1  0  0  0  0
 19 10  1  0  0  0  0
 12 20  1  4  0  0  0
 21 13  2  0  0  0  0
 22 13  1  0  0  0  0
 23  4  1  0  0  0  0
 24  5  1  0  0  0  0
 25  7  1  0  0  0  0
  8 26  1  6  0  0  0
 11 27  1  1  0  0  0
M  END


  Mrv1652305152104002D          

 27 26  0  0  1  0            999 V2000
    0.5230   -0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    6.0770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    5.6645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    3.6020    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
    2.6664    3.1895    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8099    6.9020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    4.8395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6664    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    3.6020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    7.3145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    4.4270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.5243    7.3145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    4.4270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5243    5.6645    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    6.0770    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    2.7770    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  5  4  2  0  0  0  0
  7  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  6  1  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  1  0  0  0  0
 13 11  1  0  0  0  0
  8 14  1  6  0  0  0
 15  9  2  0  0  0  0
 16  6  1  4  0  0  0
 16 10  2  0  0  0  0
 11 17  1  1  0  0  0
 17 12  2  0  0  0  0
 18  9  1  0  0  0  0
 19 10  1  0  0  0  0
 12 20  1  4  0  0  0
 21 13  2  0  0  0  0
 22 13  1  0  0  0  0
 23  4  1  0  0  0  0
 24  5  1  0  0  0  0
 25  7  1  0  0  0  0
  8 26  1  6  0  0  0
 11 27  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0009501

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C13H22N4O5/c1-3-7(2)11(13(21)22)17-12(20)8(14)6-16-10(19)5-4-9(15)18/h4-5,7-8,11H,3,6,14H2,1-2H3,(H2,15,18)(H,16,19)(H,17,20)(H,21,22)/b5-4+/t7?,8-,11-/m0/s1

> <INCHI_KEY>
WSFQKSIBZODGPB-OFANEYSTSA-N

> <FORMULA>
C13H22N4O5

> <MOLECULAR_WEIGHT>
314.342

> <EXACT_MASS>
314.159019824

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
31.955355933706535

> <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-methylpentanoic acid

> <ALOGPS_LOGP>
-2.15

> <JCHEM_LOGP>
-4.881764939608333

> <ALOGPS_LOGS>
-3.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.6260690929980646

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.21913637688117582

> <JCHEM_PKA_STRONGEST_BASIC>
12.325476727843025

> <JCHEM_POLAR_SURFACE_AREA>
172.57999999999998

> <JCHEM_REFRACTIVITY>
89.8018

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.60e-01 g/l

> <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-methylpentanoic 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       0.976  -0.976   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -0.206   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.978  11.344   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.645  10.574   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.311   6.724   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       4.977   5.954   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.978  12.884   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.645   9.034   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.977   4.414   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       3.644   6.724   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       7.645  13.654   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       6.311   8.264   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0       3.644   3.644   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0      10.312  13.654   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       8.978   8.264   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       6.311   3.644   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
HETATM   23  H   UNK     0      10.312  10.574   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       6.311  11.344   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       0.976   0.564   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       6.311   5.184   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       3.644   0.564   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    7                                                            
CONECT    3    1    7                                                       
CONECT    4    5    9   23                                                  
CONECT    5    4   10   24                                                  
CONECT    6    8   16                                                       
CONECT    7    2    3   11   25                                             
CONECT    8    6   12   14   26                                             
CONECT    9    4   15   18                                                  
CONECT   10    5   16   19                                                  
CONECT   11    7   13   17   27                                             
CONECT   12    8   17   20                                                  
CONECT   13   11   21   22                                                  
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16    6   10                                                       
CONECT   17   11   12                                                       
CONECT   18    9                                                            
CONECT   19   10                                                            
CONECT   20   12                                                            
CONECT   21   13                                                            
CONECT   22   13                                                            
CONECT   23    4                                                            
CONECT   24    5                                                            
CONECT   25    7                                                            
CONECT   26    8                                                            
CONECT   27   11                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   52    0
END

Synonyms

Value	Source
(2S)-2-{[(2S)-2-amino-1-hydroxy-3-{[(2E)-1-hydroxy-3-(C-hydroxycarbonimidoyl)prop-2-en-1-ylidene]amino}propylidene]amino}-3-methylpentanoate	Generator

Molecular Formula

C₁₃H₂₂N₄O₅

Average Mass

314.342

Monoisotopic Mass

314.159019824

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-methylpentanoic 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-methylpentanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C13H22N4O5/c1-3-7(2)11(13(21)22)17-12(20)8(14)6-16-10(19)5-4-9(15)18/h4-5,7-8,11H,3,6,14H2,1-2H3,(H2,15,18)(H,16,19)(H,17,20)(H,21,22)/b5-4+/t7?,8-,11-/m0/s1

InChI Key

WSFQKSIBZODGPB-OFANEYSTSA-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
Isoleucine or derivatives
N-acyl-alpha-amino acid
N-acyl-l-alpha-amino acid
N-acyl-alpha amino acid or derivatives
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
Amino acid or derivatives
Carboxamide group
Carboxylic acid salt
Amino acid
Primary carboxylic acid amide
Secondary carboxylic acid amide
Monocarboxylic acid or derivatives
Carboxylic acid
Organic salt
Hydrocarbon derivative
Amine
Primary aliphatic amine
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Organic oxide
Organonitrogen compound
Organooxygen compound
Primary amine
Organopnictogen compound
Organic zwitterion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.16 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-4.9	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	0.22	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	9	ChemAxon
Refractivity	89.8 m³·mol⁻¹	ChemAxon
Polarizability	31.96 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

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

58837249

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

86583460

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 B (MMDBc0009501)

MOL for #<Metabolite:0x00007f2ad48a2dd8>

3D MOL for #<Metabolite:0x00007f2ad48a2dd8>

3D SDF for #<Metabolite:0x00007f2ad48a2dd8>

3D-SDF for #<Metabolite:0x00007f2ad48a2dd8>

PDB for #<Metabolite:0x00007f2ad48a2dd8>

3D PDB for #<Metabolite:0x00007f2ad48a2dd8>

SMILES for #<Metabolite:0x00007f2ad48a2dd8>

INCHI for #<Metabolite:0x00007f2ad48a2dd8>

Structure for #<Metabolite:0x00007f2ad48a2dd8>

3D Structure for #<Metabolite:0x00007f2ad48a2dd8>