MiMeDB: Showing metabocard for pseudopaline (MMDBc0056278)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:21:36 UTC

Update Date

2025-10-07 16:09:42 UTC

Metabolite ID

MMDBc0056278

Metabolite Identification

Common Name

pseudopaline

Description

pseudopaline is a metallophore belonging to the class of opines. Its chemical structure enables it to function as a narrow spectrum ion chelator, specifically complexing with zinc ions (Zn2+). Pseudopaline is synthesized by Pseudomonas aeruginosa and plays a role in the production of polyamines and various siderophores, which are critical for metal ion acquisition in microbial environments (PMID:39155120 ). The biosynthetic pathway of pseudopaline involves gene clusters related to secondary metabolite synthesis, with seven clusters conserved across different strains of Pseudomonas (PMID:39597652 ). Additionally, it is secreted via the Drug Metabolite Transporter (DMT) family, highlighting its importance in metallophore export (PMID:37930543 ). The secretion of pseudopaline can be induced by environmental stressors such as chromium (Cr), which enhances both its production and import into bacterial cells, suggesting a role in cellular responses to metal ion availability (PMID:36099868 ). Overall, pseudopaline's ability to chelate Zn2+ is crucial for processes like transcription regulation and DNA repair in bacteria (PMID:36099868 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222212D          

 30 30  0  0  1  0            999 V2000
   -4.3523   -2.9774    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9759   -3.5174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5459   -2.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7663   -2.7073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2605   -1.8972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3575   -0.7370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2697    0.2376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1046   -1.0870    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5727   -3.2474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1695   -2.9774    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6369   -2.4373    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.7555   -3.2474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4168   -4.0575    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0136   -3.7875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7928   -3.2474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4596    0.0817    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1427   -2.1672    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6684   -0.4847    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9491   -2.7073    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3791   -3.7875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9114   -2.4373    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.6373   -4.3276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0404   -4.5976    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.2007   -4.5910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2341   -4.0575    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1691   -3.7875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5723   -3.5174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1964   -3.7875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3900   -3.2474    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4164   -2.7073    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  8  5  1  0  0  0  0
  8  6  2  0  0  0  0
  9  1  1  0  0  0  0
 10  3  1  0  0  0  0
 11  5  1  0  0  0  0
 12  2  1  0  0  0  0
 13  9  1  0  0  0  0
 14 10  1  0  0  0  0
 15 11  1  0  0  0  0
 16  6  1  0  0  0  0
 16  7  2  0  0  0  0
 17  4  1  0  0  0  0
 11 17  1  6  0  0  0
 18  7  1  0  0  0  0
 18  8  1  0  0  0  0
 19  9  1  0  0  0  0
 10 19  1  6  0  0  0
 20 12  2  0  0  0  0
 21 12  1  0  0  0  0
 22 13  2  0  0  0  0
 23 13  1  0  0  0  0
 24 14  2  0  0  0  0
 25 14  1  0  0  0  0
 26 15  2  0  0  0  0
 27 15  1  0  0  0  0
 28  9  1  0  0  0  0
 10 29  1  6  0  0  0
 11 30  1  6  0  0  0
M  CHG  2  21  -1  23  -1
M  END


  Mrv1652306172222212D          

 30 30  0  0  1  0            999 V2000
   -4.3523   -2.9774    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9759   -3.5174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5459   -2.4373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7663   -2.7073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2605   -1.8972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3575   -0.7370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2697    0.2376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1046   -1.0870    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5727   -3.2474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1695   -2.9774    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6369   -2.4373    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.7555   -3.2474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4168   -4.0575    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0136   -3.7875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7928   -3.2474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4596    0.0817    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1427   -2.1672    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6684   -0.4847    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9491   -2.7073    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3791   -3.7875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9114   -2.4373    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.6373   -4.3276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0404   -4.5976    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.2007   -4.5910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2341   -4.0575    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1691   -3.7875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5723   -3.5174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1964   -3.7875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3900   -3.2474    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4164   -2.7073    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  8  5  1  0  0  0  0
  8  6  2  0  0  0  0
  9  1  1  0  0  0  0
 10  3  1  0  0  0  0
 11  5  1  0  0  0  0
 12  2  1  0  0  0  0
 13  9  1  0  0  0  0
 14 10  1  0  0  0  0
 15 11  1  0  0  0  0
 16  6  1  0  0  0  0
 16  7  2  0  0  0  0
 17  4  1  0  0  0  0
 11 17  1  6  0  0  0
 18  7  1  0  0  0  0
 18  8  1  0  0  0  0
 19  9  1  0  0  0  0
 10 19  1  6  0  0  0
 20 12  2  0  0  0  0
 21 12  1  0  0  0  0
 22 13  2  0  0  0  0
 23 13  1  0  0  0  0
 24 14  2  0  0  0  0
 25 14  1  0  0  0  0
 26 15  2  0  0  0  0
 27 15  1  0  0  0  0
 28  9  1  0  0  0  0
 10 29  1  6  0  0  0
 11 30  1  6  0  0  0
M  CHG  2  21  -1  23  -1
M  END
> <DATABASE_ID>
MMDBc0056278

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](CC1=CN=CN1)(NCC[C@]([H])(NC([H])(CCC([O-])=O)C([O-])=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H22N4O8/c20-12(21)2-1-9(13(22)23)19-10(14(24)25)3-4-17-11(15(26)27)5-8-6-16-7-18-8/h6-7,9-11,17,19H,1-5H2,(H,16,18)(H,20,21)(H,22,23)(H,24,25)(H,26,27)/p-2/t9?,10-,11-/m0/s1

> <INCHI_KEY>
RLSXUJSGKUUKFH-DVRYWGNFSA-L

> <FORMULA>
C15H20N4O8

> <MOLECULAR_WEIGHT>
384.346

> <EXACT_MASS>
384.12921078

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
36.042044578607786

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[(1S)-1-carboxy-3-{[(1S)-1-carboxy-2-(1H-imidazol-5-yl)ethyl]amino}propyl]amino}pentanedioate

> <JCHEM_LOGP>
-8.321869974180071

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.5048434191332865

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0219721079773283

> <JCHEM_PKA_STRONGEST_BASIC>
10.257115988310696

> <JCHEM_POLAR_SURFACE_AREA>
207.59999999999997

> <JCHEM_REFRACTIVITY>
109.2964

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-{[(1S)-1-carboxy-3-{[(1S)-1-carboxy-2-(3H-imidazol-4-yl)ethyl]amino}propyl]amino}pentanedioate

> <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      -8.124  -5.558   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -9.288  -6.566   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.886  -4.550   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.430  -5.054   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.353  -3.541   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.667  -1.376   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.370   0.443   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.062  -2.029   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.669  -6.062   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.050  -5.558   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.189  -4.550   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -10.744  -6.062   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.378  -7.574   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -3.759  -7.070   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.480  -6.062   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       0.858   0.152   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0      -0.266  -4.045   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0       3.114  -0.905   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0      -5.505  -5.054   0.000  0.00  0.00           N+0
HETATM   20  O   UNK     0     -11.908  -7.070   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0     -11.035  -4.550   0.000  0.00  0.00           O-1
HETATM   22  O   UNK     0      -4.923  -8.078   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -7.542  -8.582   0.000  0.00  0.00           O-1
HETATM   24  O   UNK     0      -4.108  -8.570   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -2.304  -7.574   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.316  -7.070   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       2.935  -6.566   0.000  0.00  0.00           O+0
HETATM   28  H   UNK     0      -7.833  -7.070   0.000  0.00  0.00           H+0
HETATM   29  H   UNK     0      -2.595  -6.062   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0       2.644  -5.054   0.000  0.00  0.00           H+0
CONECT    1    2    9                                                       
CONECT    2    1   12                                                       
CONECT    3    4   10                                                       
CONECT    4    3   17                                                       
CONECT    5    8   11                                                       
CONECT    6    8   16                                                       
CONECT    7   16   18                                                       
CONECT    8    5    6   18                                                  
CONECT    9    1   13   19   28                                             
CONECT   10    3   14   19   29                                             
CONECT   11    5   15   17   30                                             
CONECT   12    2   20   21                                                  
CONECT   13    9   22   23                                                  
CONECT   14   10   24   25                                                  
CONECT   15   11   26   27                                                  
CONECT   16    6    7                                                       
CONECT   17    4   11                                                       
CONECT   18    7    8                                                       
CONECT   19    9   10                                                       
CONECT   20   12                                                            
CONECT   21   12                                                            
CONECT   22   13                                                            
CONECT   23   13                                                            
CONECT   24   14                                                            
CONECT   25   14                                                            
CONECT   26   15                                                            
CONECT   27   15                                                            
CONECT   28    9                                                            
CONECT   29   10                                                            
CONECT   30   11                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   60    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₂₀N₄O₈

Average Mass

384.346

Monoisotopic Mass

384.12921078

IUPAC Name

2-{[(1S)-1-carboxy-3-{[(1S)-1-carboxy-2-(1H-imidazol-5-yl)ethyl]amino}propyl]amino}pentanedioate

Traditional Name

2-{[(1S)-1-carboxy-3-{[(1S)-1-carboxy-2-(3H-imidazol-4-yl)ethyl]amino}propyl]amino}pentanedioate

CAS Registry Number

Not Available

SMILES

[H][C@@](CC1=CN=CN1)(NCC[C@]([H])(NC([H])(CCC([O-])=O)C([O-])=O)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C15H22N4O8/c20-12(21)2-1-9(13(22)23)19-10(14(24)25)3-4-17-11(15(26)27)5-8-6-16-7-18-8/h6-7,9-11,17,19H,1-5H2,(H,16,18)(H,20,21)(H,22,23)(H,24,25)(H,26,27)/p-2/t9?,10-,11-/m0/s1

InChI Key

RLSXUJSGKUUKFH-DVRYWGNFSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Histidine and derivatives

Alternative Parents

Substituents

Histidine or derivatives
Glutamic acid or derivatives
Tetracarboxylic acid or derivatives
L-alpha-amino acid
Alpha-amino acid
Imidazolyl carboxylic acid derivative
Aralkylamine
Amino fatty acid
Fatty acyl
Heteroaromatic compound
Imidazole
Azole
Amino acid
Azacycle
Organoheterocyclic compound
Secondary amine
Secondary aliphatic amine
Carboxylic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-8.3	ChemAxon
pKa (Strongest Acidic)	1.02	ChemAxon
pKa (Strongest Basic)	10.26	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	207.6 Å²	ChemAxon
Rotatable Bond Count	14	ChemAxon
Refractivity	109.3 m³·mol⁻¹	ChemAxon
Polarizability	36.04 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

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

Not Available

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/Eubacteria	Proteobacteria	2	Human

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

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

134820325

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 pseudopaline (MMDBc0056278)

MOL for #<Metabolite:0x00007fadd83733f8>

3D MOL for #<Metabolite:0x00007fadd83733f8>

3D SDF for #<Metabolite:0x00007fadd83733f8>

3D-SDF for #<Metabolite:0x00007fadd83733f8>

PDB for #<Metabolite:0x00007fadd83733f8>

3D PDB for #<Metabolite:0x00007fadd83733f8>

SMILES for #<Metabolite:0x00007fadd83733f8>

INCHI for #<Metabolite:0x00007fadd83733f8>

Structure for #<Metabolite:0x00007fadd83733f8>

3D Structure for #<Metabolite:0x00007fadd83733f8>