MiMeDB: Showing metabocard for Pyochelin (MMDBc0013436)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 04:45:23 UTC

Update Date

2022-08-31 06:36:08 UTC

Metabolite ID

MMDBc0013436

Metabolite Identification

Common Name

Pyochelin

Description

pyochelin I belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. The enantiomeric compounds, enant-pyochelin I and II, are produced by Pseudomonas fluorescens. Pseudomonas aeruginosa produces a mixture of pyochelin I (major) and pyochelin II (minor) via condensation of salicylic acid and two molecules of cysteine. pyochelin I is a strong basic compound (based on its pKa). A pyochelin that has R-stereochemistry at the thioaminal centre; the diastereoisomer with S-stereochemistry at this centre is pyochelin II.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05031422072D          

 24 26  0  0  1  0            999 V2000
   -0.7376    4.5211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884    0.9479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1528    0.1942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034    1.6153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3323    0.1080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    2.9812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    5.5606    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830    1.5291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.4661    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3020    5.5606    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1526    0.7754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    2.1965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.2911    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1830    6.2281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    2.9812    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    4.7760    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9731    0.6892    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034    6.1418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1526    6.9817    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    2.1965    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    4.7760    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4496    3.8406    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6765    6.2957    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0206    3.9165    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  8  4  2  0  0  0  0
  9  6  1  0  0  0  0
 10  7  1  0  0  0  0
 11  5  2  0  0  0  0
 11  8  1  0  0  0  0
 12  8  1  0  0  0  0
  9 13  1  1  0  0  0
 10 14  1  6  0  0  0
 15  9  1  0  0  0  0
 15 12  2  0  0  0  0
 16  1  1  0  0  0  0
 16 10  1  0  0  0  0
 16 13  1  0  0  0  0
 17 11  1  0  0  0  0
 18 14  2  0  0  0  0
 19 14  1  0  0  0  0
 20  6  1  0  0  0  0
 20 12  1  0  0  0  0
 21  7  1  0  0  0  0
 21 13  1  0  0  0  0
  9 22  1  6  0  0  0
 10 23  1  1  0  0  0
 13 24  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0013436

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CS[C@@]([H])(N1C)[C@@]1([H])CSC(=N1)C1=CC=CC=C1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H16N2O3S2/c1-16-10(14(18)19)7-21-13(16)9-6-20-12(15-9)8-4-2-3-5-11(8)17/h2-5,9-10,13,17H,6-7H2,1H3,(H,18,19)/t9-,10+,13-/m1/s1

> <INCHI_KEY>
NYBZAGXTZXPYND-GBIKHYSHSA-N

> <FORMULA>
C14H16N2O3S2

> <MOLECULAR_WEIGHT>
324.418

> <EXACT_MASS>
324.060233768

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
32.15214789292467

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,4R)-2-[(4R)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-3-methyl-1,3-thiazolidine-4-carboxylic acid

> <ALOGPS_LOGP>
1.49

> <JCHEM_LOGP>
1.7453949831981777

> <ALOGPS_LOGS>
-3.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.618344340683885

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.683771769768955

> <JCHEM_PKA_STRONGEST_BASIC>
4.71190963912994

> <JCHEM_POLAR_SURFACE_AREA>
73.13

> <JCHEM_REFRACTIVITY>
85.2026

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.07e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,4R)-2-[(4R)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-3-methyl-1,3-thiazolidine-4-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   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       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       0.000   0.000   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       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM   21  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM   22  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1   16                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    8                                                       
CONECT    5    3   11                                                       
CONECT    6    9   20                                                       
CONECT    7   10   21                                                       
CONECT    8    4   11   12                                                  
CONECT    9    6   13   15   22                                             
CONECT   10    7   14   16   23                                             
CONECT   11    5    8   17                                                  
CONECT   12    8   15   20                                                  
CONECT   13    9   16   21   24                                             
CONECT   14   10   18   19                                                  
CONECT   15    9   12                                                       
CONECT   16    1   10   13                                                  
CONECT   17   11                                                            
CONECT   18   14                                                            
CONECT   19   14                                                            
CONECT   20    6   12                                                       
CONECT   21    7   13                                                       
CONECT   22    9                                                            
CONECT   23   10                                                            
CONECT   24   13                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

Synonyms

Value	Source
(4'r,2''R,4''r)-2'-(2-hydroxyphenyl)-3''-methyl-2'',3'',4'',4',5'-hexahydro-[2,4']-bisthiazolyl-4''-carboxylic acid	ChEBI
(4'r,2''R,4''r)-2'-(2-hydroxyphenyl)-3''-methyl-2'',3'',4'',4',5'-hexahydro-[2,4']-bisthiazolyl-4''-carboxylate	Generator
Pyochelin	MeSH

Molecular Formula

C₁₄H₁₆N₂O₃S₂

Average Mass

324.418

Monoisotopic Mass

324.060233768

IUPAC Name

(2R,4R)-2-[(4R)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-3-methyl-1,3-thiazolidine-4-carboxylic acid

Traditional Name

(2R,4R)-2-[(4R)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-3-methyl-1,3-thiazolidine-4-carboxylic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(CS[C@@]([H])(N1C)[C@@]1([H])CSC(=N1)C1=CC=CC=C1O)C(O)=O

InChI Identifier

InChI=1S/C14H16N2O3S2/c1-16-10(14(18)19)7-21-13(16)9-6-20-12(15-9)8-4-2-3-5-11(8)17/h2-5,9-10,13,17H,6-7H2,1H3,(H,18,19)/t9-,10+,13-/m1/s1

InChI Key

NYBZAGXTZXPYND-GBIKHYSHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Benzenoid
Imidothiolactone
Thiazolidine
Meta-thiazoline
Carboxylic acid
Monocarboxylic acid or derivatives
Thioether
Hemithioaminal
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Dialkylthioether
Azacycle
Organoheterocyclic compound
Organic oxide
Carbonyl group
Hydrocarbon derivative
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Organopnictogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyochelin (CHEBI:67183 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.31 g/L	ALOGPS
logP	1.49	ALOGPS
logP	1.75	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	2.68	ChemAxon
pKa (Strongest Basic)	4.71	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	73.13 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	85.2 m³·mol⁻¹	ChemAxon
Polarizability	32.15 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

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/Eubacteria	Proteobacteria	1	Human ; Human sputum; Human subgingival plaque; Human feces	Metabolic reconstruction
Bacteria	nah	1		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

CPD-9992

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5287441

PDB ID

Not Available

ChEBI ID

67183

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 Pyochelin (MMDBc0013436)

MOL for #<Metabolite:0x00007f91dd2eb050>

3D MOL for #<Metabolite:0x00007f91dd2eb050>

3D SDF for #<Metabolite:0x00007f91dd2eb050>

3D-SDF for #<Metabolite:0x00007f91dd2eb050>

PDB for #<Metabolite:0x00007f91dd2eb050>

3D PDB for #<Metabolite:0x00007f91dd2eb050>

SMILES for #<Metabolite:0x00007f91dd2eb050>

INCHI for #<Metabolite:0x00007f91dd2eb050>

Structure for #<Metabolite:0x00007f91dd2eb050>

3D Structure for #<Metabolite:0x00007f91dd2eb050>