MiMeDB: Showing metabocard for Delftibactin B (MMDBc0024707)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 14:30:31 UTC

Update Date

2022-08-31 06:49:56 UTC

Metabolite ID

MMDBc0024707

Metabolite Identification

Common Name

Delftibactin B

Description

Delftibactin B belongs to the class of organic compounds known as hybrid peptides. Hybrid peptides are compounds containing at least two different types of amino acids (alpha, beta, gamma, delta) linked to each other through a peptide bond. Based on a literature review very few articles have been published on Delftibactin B.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152116302D          

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M  END


  Mrv1652305152116302D          

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 52 38  2  0  0  0  0
 53 29  1  4  0  0  0
 53 32  2  0  0  0  0
 54 14  1  0  0  0  0
 54 21  1  0  0  0  0
 55 15  1  0  0  0  0
 55 39  1  0  0  0  0
 56 17  1  0  0  0  0
 57 20  1  0  0  0  0
 58 21  2  0  0  0  0
 59 27  1  0  0  0  0
 60 30  1  0  0  0  0
 61 31  1  0  0  0  0
 62 32  1  0  0  0  0
 63 33  1  0  0  0  0
 64 34  1  0  0  0  0
 65 35  1  0  0  0  0
 66 36  1  0  0  0  0
 67 37  1  0  0  0  0
 68 38  1  0  0  0  0
 69 39  2  0  0  0  0
 70 40  2  0  0  0  0
 71 40  1  0  0  0  0
 72 54  1  0  0  0  0
 73 55  1  0  0  0  0
 74  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0024707

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(C)=C(\N=C(O)CN=C(O)C(N=C(O)C(N=C(O)C(C)C(O)C(C)N)C(O)C(O)=O)C(C)O)C(O)=NC(CCCN(O)C(C)=O)C(O)=NC(CO)C(O)=NC(CCCNC(N)=N)C(O)=NC1CCCN(O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C41H70N14O18/c1-6-22(47-27(59)16-46-37(67)28(20(4)57)52-38(68)29(31(61)40(70)71)53-32(62)18(2)30(60)19(3)42)33(63)48-24(11-8-14-54(72)21(5)58)35(65)51-26(17-56)36(66)49-23(10-7-13-45-41(43)44)34(64)50-25-12-9-15-55(73)39(25)69/h6,18-20,23-26,28-31,56-57,60-61,72-73H,7-17,42H2,1-5H3,(H,46,67)(H,47,59)(H,48,63)(H,49,66)(H,50,64)(H,51,65)(H,52,68)(H,53,62)(H,70,71)(H4,43,44,45)/b22-6-

> <INCHI_KEY>
YHBAYFBDFCGZTI-HCDFXORVSA-N

> <FORMULA>
C41H70N14O18

> <MOLECULAR_WEIGHT>
1047.091

> <EXACT_MASS>
1046.49925147

> <JCHEM_ACCEPTOR_COUNT>
30

> <JCHEM_ATOM_COUNT>
143

> <JCHEM_AVERAGE_POLARIZABILITY>
101.62850919289633

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
19

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(4-amino-1,3-dihydroxy-2-methylpentylidene)amino]-3-({1-[({[(1Z)-1-[(1-{[1-({4-carbamimidamido-1-[(1-hydroxy-2-oxopiperidin-3-yl)-C-hydroxycarbonimidoyl]butyl}-C-hydroxycarbonimidoyl)-2-hydroxyethyl]-C-hydroxycarbonimidoyl}-4-(N-hydroxyacetamido)butyl)-C-hydroxycarbonimidoyl]prop-1-en-1-yl]-C-hydroxycarbonimidoyl}methyl)-C-hydroxycarbonimidoyl]-2-hydroxypropyl}-C-hydroxycarbonimidoyl)-2-hydroxypropanoic acid

> <ALOGPS_LOGP>
-0.76

> <JCHEM_LOGP>
-5.870774837562531

> <ALOGPS_LOGS>
-3.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.9432498811858085

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.4873940261195986

> <JCHEM_PKA_STRONGEST_BASIC>
11.901627972051093

> <JCHEM_POLAR_SURFACE_AREA>
547.9400000000003

> <JCHEM_REFRACTIVITY>
263.3111000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
30

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.78e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(4-amino-1,3-dihydroxy-2-methylpentylidene)amino]-3-({1-[({[(1Z)-1-[(1-{[1-({4-carbamimidamido-1-[(1-hydroxy-2-oxopiperidin-3-yl)-C-hydroxycarbonimidoyl]butyl}-C-hydroxycarbonimidoyl)-2-hydroxyethyl]-C-hydroxycarbonimidoyl}-4-(N-hydroxyacetamido)butyl)-C-hydroxycarbonimidoyl]prop-1-en-1-yl]-C-hydroxycarbonimidoyl}methyl)-C-hydroxycarbonimidoyl]-2-hydroxypropyl}-C-hydroxycarbonimidoyl)-2-hydroxypropanoic 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      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -8.002   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.000 -12.320   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.000  -7.700   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -8.002   1.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -5.335   6.160   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -6.668   6.930   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -8.002   6.160   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      13.337   0.000   0.000  0.00  0.00           C+0
HETATM   42  N   UNK     0       1.334   8.470   0.000  0.00  0.00           N+0
HETATM   43  N   UNK     0      13.337   1.540   0.000  0.00  0.00           N+0
HETATM   44  N   UNK     0      14.670  -0.770   0.000  0.00  0.00           N+0
HETATM   45  N   UNK     0      12.003  -0.770   0.000  0.00  0.00           N+0
HETATM   46  N   UNK     0      -5.335   0.000   0.000  0.00  0.00           N+0
HETATM   47  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
HETATM   48  N   UNK     0      -0.000  -4.620   0.000  0.00  0.00           N+0
HETATM   49  N   UNK     0       6.668  -2.310   0.000  0.00  0.00           N+0
HETATM   50  N   UNK     0       4.001  -0.770   0.000  0.00  0.00           N+0
HETATM   51  N   UNK     0       4.001  -5.390   0.000  0.00  0.00           N+0
HETATM   52  N   UNK     0      -6.668   3.850   0.000  0.00  0.00           N+0
HETATM   53  N   UNK     0      -4.001   6.930   0.000  0.00  0.00           N+0
HETATM   54  N   UNK     0      -1.334 -10.010   0.000  0.00  0.00           N+0
HETATM   55  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM   56  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      -9.336   2.310   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      -2.667 -12.320   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      -6.668   8.470   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      -4.001   3.850   0.000  0.00  0.00           O+0
HETATM   69  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   70  O   UNK     0      -8.002   4.620   0.000  0.00  0.00           O+0
HETATM   71  O   UNK     0      -9.336   6.930   0.000  0.00  0.00           O+0
HETATM   72  O   UNK     0      -2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   73  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   74  H   UNK     0      -2.667  -4.620   0.000  0.00  0.00           H+0
CONECT    1    6                                                            
CONECT    2   18                                                            
CONECT    3   19                                                            
CONECT    4   20                                                            
CONECT    5   21                                                            
CONECT    6    1   22   74                                                  
CONECT    7   10   13                                                       
CONECT    8   11   14                                                       
CONECT    9   12   15                                                       
CONECT   10    7   23                                                       
CONECT   11    8   24                                                       
CONECT   12    9   25                                                       
CONECT   13    7   45                                                       
CONECT   14    8   54                                                       
CONECT   15    9   55                                                       
CONECT   16   27   46                                                       
CONECT   17   26   56                                                       
CONECT   18    2   30   32                                                  
CONECT   19    3   30   42                                                  
CONECT   20    4   28   57                                                  
CONECT   21    5   54   58                                                  
CONECT   22    6   33   47                                                  
CONECT   23   10   34   49                                                  
CONECT   24   11   35   48                                                  
CONECT   25   12   39   50                                                  
CONECT   26   17   36   51                                                  
CONECT   27   16   47   59                                                  
CONECT   28   20   37   52                                                  
CONECT   29   31   38   53                                                  
CONECT   30   18   19   60                                                  
CONECT   31   29   40   61                                                  
CONECT   32   18   53   62                                                  
CONECT   33   22   48   63                                                  
CONECT   34   23   50   64                                                  
CONECT   35   24   51   65                                                  
CONECT   36   26   49   66                                                  
CONECT   37   28   46   67                                                  
CONECT   38   29   52   68                                                  
CONECT   39   25   55   69                                                  
CONECT   40   31   70   71                                                  
CONECT   41   43   44   45                                                  
CONECT   42   19                                                            
CONECT   43   41                                                            
CONECT   44   41                                                            
CONECT   45   13   41                                                       
CONECT   46   16   37                                                       
CONECT   47   22   27                                                       
CONECT   48   24   33                                                       
CONECT   49   23   36                                                       
CONECT   50   25   34                                                       
CONECT   51   26   35                                                       
CONECT   52   28   38                                                       
CONECT   53   29   32                                                       
CONECT   54   14   21   72                                                  
CONECT   55   15   39   73                                                  
CONECT   56   17                                                            
CONECT   57   20                                                            
CONECT   58   21                                                            
CONECT   59   27                                                            
CONECT   60   30                                                            
CONECT   61   31                                                            
CONECT   62   32                                                            
CONECT   63   33                                                            
CONECT   64   34                                                            
CONECT   65   35                                                            
CONECT   66   36                                                            
CONECT   67   37                                                            
CONECT   68   38                                                            
CONECT   69   39                                                            
CONECT   70   40                                                            
CONECT   71   40                                                            
CONECT   72   54                                                            
CONECT   73   55                                                            
CONECT   74    6                                                            
MASTER        0    0    0    0    0    0    0    0   74    0  148    0
END

Synonyms

Not Available

Molecular Formula

C₄₁H₇₀N₁₄O₁₈

Average Mass

1047.091

Monoisotopic Mass

1046.49925147

IUPAC Name

3-[(4-amino-1,3-dihydroxy-2-methylpentylidene)amino]-3-({1-[({[(1Z)-1-[(1-{[1-({4-carbamimidamido-1-[(1-hydroxy-2-oxopiperidin-3-yl)-C-hydroxycarbonimidoyl]butyl}-C-hydroxycarbonimidoyl)-2-hydroxyethyl]-C-hydroxycarbonimidoyl}-4-(N-hydroxyacetamido)butyl)-C-hydroxycarbonimidoyl]prop-1-en-1-yl]-C-hydroxycarbonimidoyl}methyl)-C-hydroxycarbonimidoyl]-2-hydroxypropyl}-C-hydroxycarbonimidoyl)-2-hydroxypropanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

[H]\C(C)=C(\N=C(O)CN=C(O)C(N=C(O)C(N=C(O)C(C)C(O)C(C)N)C(O)C(O)=O)C(C)O)C(O)=NC(CCCN(O)C(C)=O)C(O)=NC(CO)C(O)=NC(CCCNC(N)=N)C(O)=NC1CCCN(O)C1=O

InChI Identifier

InChI=1S/C41H70N14O18/c1-6-22(47-27(59)16-46-37(67)28(20(4)57)52-38(68)29(31(61)40(70)71)53-32(62)18(2)30(60)19(3)42)33(63)48-24(11-8-14-54(72)21(5)58)35(65)51-26(17-56)36(66)49-23(10-7-13-45-41(43)44)34(64)50-25-12-9-15-55(73)39(25)69/h6,18-20,23-26,28-31,56-57,60-61,72-73H,7-17,42H2,1-5H3,(H,46,67)(H,47,59)(H,48,63)(H,49,66)(H,50,64)(H,51,65)(H,52,68)(H,53,62)(H,70,71)(H4,43,44,45)/b22-6-

InChI Key

YHBAYFBDFCGZTI-HCDFXORVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hybrid peptides. Hybrid peptides are compounds containing at least two different types of amino acids (alpha, beta, gamma, delta) linked to each other through a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Peptidomimetics

Sub Class

Hybrid peptides

Direct Parent

Hybrid peptides

Alternative Parents

Substituents

Hybrid peptide
Aspartic acid or derivatives
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Serine or derivatives
Gamma amino acid or derivatives
N-substituted-alpha-amino acid
Alpha-amino acid or derivatives
Hydroxy fatty acid
Heterocyclic fatty acid
Piperidinone
Delta-lactam
Branched fatty acid
Hydroxy acid
Monosaccharide
N-acyl-amine
Alpha-hydroxy acid
Piperidine
Fatty amide
Fatty acyl
Acetohydroxamic acid
Acetamide
Lactam
Amino acid or derivatives
Hydroxamic acid
Guanidine
Secondary alcohol
Secondary carboxylic acid amide
1,2-aminoalcohol
Amino acid
Carboxamide group
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Carboxylic acid derivative
Carboxylic acid
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Monocarboxylic acid or derivatives
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Alcohol
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Amine
Primary aliphatic amine
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	0.18 g/L	ALOGPS
logP	-0.76	ALOGPS
logP	-5.9	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	2.49	ChemAxon
pKa (Strongest Basic)	11.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	30	ChemAxon
Hydrogen Donor Count	19	ChemAxon
Polar Surface Area	547.94 Å²	ChemAxon
Rotatable Bond Count	30	ChemAxon
Refractivity	263.31 m³·mol⁻¹	ChemAxon
Polarizability	101.63 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	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

Metabolic Reactions

Not Available

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

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

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

70680459

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 Delftibactin B (MMDBc0024707)

MOL for #<Metabolite:0x00007fdb463a1870>

3D MOL for #<Metabolite:0x00007fdb463a1870>

3D SDF for #<Metabolite:0x00007fdb463a1870>

3D-SDF for #<Metabolite:0x00007fdb463a1870>

PDB for #<Metabolite:0x00007fdb463a1870>

3D PDB for #<Metabolite:0x00007fdb463a1870>

SMILES for #<Metabolite:0x00007fdb463a1870>

INCHI for #<Metabolite:0x00007fdb463a1870>

Structure for #<Metabolite:0x00007fdb463a1870>

3D Structure for #<Metabolite:0x00007fdb463a1870>