MiMeDB: Showing metabocard for yersinopine (MMDBc0056381)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:24:13 UTC

Update Date

2025-10-07 16:09:46 UTC

Metabolite ID

MMDBc0056381

Metabolite Identification

Common Name

yersinopine

Description

yersinopine is a metallophore belonging to the opine chemical class, primarily synthesized by the bacterium Yersinia pestis. Its chemical structure is characterized by a unique arrangement of functional groups that facilitate metal ion binding, crucial for its role in iron acquisition. Yersinopine shares structural similarities with other opines such as staphylopine and pseudopaline, which are produced by Staphylococcus aureus and Pseudomonas aeruginosa, respectively (PMID:37106798 ). The biosynthesis of yersinopine involves opine dehydrogenases (ODHs), which catalyze the final enzymatic step in the formation of this metallophore (PMID:29618515 ). Additionally, yersinopine is implicated in the synthesis of ririwpeptides and is part of a broader network of metallophore production in pathogenic bacteria (PMID:37967102 ). This compound plays a significant role in the iron acquisition pathways of Yersinia pestis, enhancing its virulence and survival in host environments (PMID:33084706 ). Overall, yersinopine exemplifies the intricate biochemical strategies employed by bacteria to thrive in iron-limited conditions.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222242D          

 26 26  0  0  1  0            999 V2000
    6.5599    0.4317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7765   -1.2844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9838   -1.0556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0022   -1.9709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5586   -2.2488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1043   -0.9936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7581   -0.3692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2096   -1.7421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3709   -0.7124    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5967   -1.3988    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.5507   -0.5980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1728    0.0884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3986   -0.5980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1245   -1.7863    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3894   -1.6277    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9288   -0.9663    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1636   -0.9412    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.1452   -0.0260    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7488   -1.3988    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.7673    0.6605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3802    0.3173    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6059   -0.3692    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9930   -0.0260    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3525    0.2029    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5783   -0.4836    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8041   -1.1700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  7  1  1  0  0  0  0
  8  4  1  0  0  0  0
  8  5  2  0  0  0  0
  9  2  1  0  0  0  0
 10  4  1  0  0  0  0
 11  7  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14  5  1  0  0  0  0
 14  6  2  0  0  0  0
 15  3  1  0  0  0  0
 10 15  1  6  0  0  0
 16  6  1  0  0  0  0
 16  8  1  0  0  0  0
 17  7  1  0  0  0  0
  9 17  1  6  0  0  0
 18 11  2  0  0  0  0
 19 11  1  0  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  7  1  0  0  0  0
  9 25  1  6  0  0  0
 10 26  1  6  0  0  0
M  CHG  1  19  -1
M  END


  Mrv1652306172222242D          

 26 26  0  0  1  0            999 V2000
    6.5599    0.4317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7765   -1.2844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9838   -1.0556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0022   -1.9709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5586   -2.2488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1043   -0.9936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7581   -0.3692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2096   -1.7421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3709   -0.7124    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5967   -1.3988    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.5507   -0.5980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1728    0.0884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3986   -0.5980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1245   -1.7863    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3894   -1.6277    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9288   -0.9663    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1636   -0.9412    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.1452   -0.0260    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7488   -1.3988    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.7673    0.6605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3802    0.3173    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6059   -0.3692    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9930   -0.0260    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3525    0.2029    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5783   -0.4836    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8041   -1.1700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  7  1  1  0  0  0  0
  8  4  1  0  0  0  0
  8  5  2  0  0  0  0
  9  2  1  0  0  0  0
 10  4  1  0  0  0  0
 11  7  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14  5  1  0  0  0  0
 14  6  2  0  0  0  0
 15  3  1  0  0  0  0
 10 15  1  6  0  0  0
 16  6  1  0  0  0  0
 16  8  1  0  0  0  0
 17  7  1  0  0  0  0
  9 17  1  6  0  0  0
 18 11  2  0  0  0  0
 19 11  1  0  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  7  1  0  0  0  0
  9 25  1  6  0  0  0
 10 26  1  6  0  0  0
M  CHG  1  19  -1
M  END
> <DATABASE_ID>
MMDBc0056381

> <DATABASE_NAME>
MIME

> <SMILES>
[H]C(C)(N[C@@]([H])(CCN[C@@]([H])(CC1=CN=CN1)C(O)=O)C(O)=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H20N4O6/c1-7(11(18)19)17-9(12(20)21)2-3-15-10(13(22)23)4-8-5-14-6-16-8/h5-7,9-10,15,17H,2-4H2,1H3,(H,14,16)(H,18,19)(H,20,21)(H,22,23)/p-1/t7?,9-,10-/m0/s1

> <INCHI_KEY>
WLNNYKMTYVPSDL-IVNRZZHDSA-M

> <FORMULA>
C13H19N4O6

> <MOLECULAR_WEIGHT>
327.318

> <EXACT_MASS>
327.131007928

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
31.62732961890822

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-8.286000496726318

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.608648991626944

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0883145524674358

> <JCHEM_PKA_STRONGEST_BASIC>
10.247816907325506

> <JCHEM_POLAR_SURFACE_AREA>
167.46999999999997

> <JCHEM_REFRACTIVITY>
87.6689

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

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

> <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      12.245   0.806   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.916  -2.398   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.436  -1.970   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.738  -3.679   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.043  -4.198   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.195  -1.855   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.615  -0.689   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.258  -3.252   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.026  -1.330   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.847  -2.611   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.095  -1.116   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.656   0.165   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.477  -1.116   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -0.232  -3.334   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       6.327  -3.038   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       1.734  -1.804   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0      11.505  -1.757   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0      15.204  -0.048   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      14.465  -2.611   0.000  0.00  0.00           O-1
HETATM   20  O   UNK     0      10.766   1.233   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       8.176   0.592   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       2.998  -0.689   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       5.587  -0.048   0.000  0.00  0.00           O+0
HETATM   24  H   UNK     0      13.725   0.379   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       8.546  -0.903   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       3.368  -2.184   0.000  0.00  0.00           H+0
CONECT    1    7                                                            
CONECT    2    3    9                                                       
CONECT    3    2   15                                                       
CONECT    4    8   10                                                       
CONECT    5    8   14                                                       
CONECT    6   14   16                                                       
CONECT    7    1   11   17   24                                             
CONECT    8    4    5   16                                                  
CONECT    9    2   12   17   25                                             
CONECT   10    4   13   15   26                                             
CONECT   11    7   18   19                                                  
CONECT   12    9   20   21                                                  
CONECT   13   10   22   23                                                  
CONECT   14    5    6                                                       
CONECT   15    3   10                                                       
CONECT   16    6    8                                                       
CONECT   17    7    9                                                       
CONECT   18   11                                                            
CONECT   19   11                                                            
CONECT   20   12                                                            
CONECT   21   12                                                            
CONECT   22   13                                                            
CONECT   23   13                                                            
CONECT   24    7                                                            
CONECT   25    9                                                            
CONECT   26   10                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   52    0
END

Synonyms

Not Available

Molecular Formula

C₁₃H₁₉N₄O₆

Average Mass

327.318

Monoisotopic Mass

327.131007928

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

[H]C(C)(N[C@@]([H])(CCN[C@@]([H])(CC1=CN=CN1)C(O)=O)C(O)=O)C([O-])=O

InChI Identifier

InChI=1S/C13H20N4O6/c1-7(11(18)19)17-9(12(20)21)2-3-15-10(13(22)23)4-8-5-14-6-16-8/h5-7,9-10,15,17H,2-4H2,1H3,(H,14,16)(H,18,19)(H,20,21)(H,22,23)/p-1/t7?,9-,10-/m0/s1

InChI Key

WLNNYKMTYVPSDL-IVNRZZHDSA-M

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
Alanine or derivatives
L-alpha-amino acid
Alpha-amino acid
Tricarboxylic acid or derivatives
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)	1.09	ChemAxon
pKa (Strongest Basic)	10.25	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	167.47 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	87.67 m³·mol⁻¹	ChemAxon
Polarizability	31.63 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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	1	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

134820225

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 yersinopine (MMDBc0056381)

MOL for #<Metabolite:0x00007fae03b40a10>

3D MOL for #<Metabolite:0x00007fae03b40a10>

3D SDF for #<Metabolite:0x00007fae03b40a10>

3D-SDF for #<Metabolite:0x00007fae03b40a10>

PDB for #<Metabolite:0x00007fae03b40a10>

3D PDB for #<Metabolite:0x00007fae03b40a10>

SMILES for #<Metabolite:0x00007fae03b40a10>

INCHI for #<Metabolite:0x00007fae03b40a10>

Structure for #<Metabolite:0x00007fae03b40a10>

3D Structure for #<Metabolite:0x00007fae03b40a10>