MiMeDB: Showing metabocard for Ni(II)-pyridinium-3,5-bisthiocarboxylic acid mononucleotide (MMDBc0056218)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:19:48 UTC

Update Date

2022-08-12 20:09:38 UTC

Metabolite ID

MMDBc0056218

Metabolite Identification

Common Name

Ni(II)-pyridinium-3,5-bisthiocarboxylic acid mononucleotide

Description

Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide(1-) belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups. Based on a literature review very few articles have been published on Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide(1-).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222192D          

 30 30  0  0  1  0            999 V2000
    0.8839   -0.9817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -0.4005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0333    0.4394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7044   -1.0679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -0.2280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7512    2.2902    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0837    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387    1.0206    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0399   -1.8216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2721   -0.1418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538    0.3532    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.7512    3.1152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5550   -2.4890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6077    0.6119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    0.9785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3856    2.0180    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3460    2.5477    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.8163    1.5082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637    1.0206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6010    1.7631    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.8604   -1.9078    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7571   -0.8092    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    7.1702    2.2730    0.0000 Ni  0  3  0  0  0  0  0  0  0  0  0  0
    3.5477    2.6201    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0161    2.6647    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5004    1.2219    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7132    0.2856    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  2  0  0  0  0
  5  2  1  0  0  0  0
  6  1  2  0  0  0  0
  6  3  1  0  0  0  0
  7  4  1  1  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  2  2  0  0  0  0
 13  3  1  0  0  0  0
 10 13  1  1  0  0  0
  8 14  1  6  0  0  0
  9 15  1  6  0  0  0
 16 11  2  0  0  0  0
 17 12  2  0  0  0  0
 21  4  1  0  0  0  0
 22  7  1  0  0  0  0
 22 10  1  0  0  0  0
 23 18  2  0  0  0  0
 23 19  1  0  0  0  0
 23 20  1  0  0  0  0
 23 21  1  0  0  0  0
 24 11  1  0  0  0  0
 25 12  1  0  0  0  0
  7 27  1  6  0  0  0
  8 28  1  1  0  0  0
  9 29  1  1  0  0  0
 10 30  1  6  0  0  0
M  CHG  5  13   1  19  -1  20  -1  25  -1  26   1
M  RAD  1   3   2
M  END


  Mrv1652306172222192D          

 30 30  0  0  1  0            999 V2000
    0.8839   -0.9817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -0.4005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0333    0.4394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7044   -1.0679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -0.2280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7512    2.2902    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0837    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387    1.0206    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0399   -1.8216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2721   -0.1418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538    0.3532    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.7512    3.1152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2991    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5550   -2.4890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6077    0.6119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    0.9785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3856    2.0180    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3460    2.5477    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.8163    1.5082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637    1.0206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6010    1.7631    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.8604   -1.9078    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7571   -0.8092    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    7.1702    2.2730    0.0000 Ni  0  3  0  0  0  0  0  0  0  0  0  0
    3.5477    2.6201    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0161    2.6647    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5004    1.2219    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7132    0.2856    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  2  0  0  0  0
  5  2  1  0  0  0  0
  6  1  2  0  0  0  0
  6  3  1  0  0  0  0
  7  4  1  1  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  2  2  0  0  0  0
 13  3  1  0  0  0  0
 10 13  1  1  0  0  0
  8 14  1  6  0  0  0
  9 15  1  6  0  0  0
 16 11  2  0  0  0  0
 17 12  2  0  0  0  0
 21  4  1  0  0  0  0
 22  7  1  0  0  0  0
 22 10  1  0  0  0  0
 23 18  2  0  0  0  0
 23 19  1  0  0  0  0
 23 20  1  0  0  0  0
 23 21  1  0  0  0  0
 24 11  1  0  0  0  0
 25 12  1  0  0  0  0
  7 27  1  6  0  0  0
  8 28  1  1  0  0  0
  9 29  1  1  0  0  0
 10 30  1  6  0  0  0
M  CHG  5  13   1  19  -1  20  -1  25  -1  26   1
M  RAD  1   3   2
M  END
> <DATABASE_ID>
MMDBc0056218

> <DATABASE_NAME>
MIME

> <SMILES>
[Ni+].[H][C@]1(O)[C@@]([H])(O)[C@@]([H])(O[C@]1([H])COP([O-])([O-])=O)[N+]1=CC(=C=C([CH]1)C([S-])=O)C(S)=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H13NO9PS2.Ni/c14-8-7(4-21-23(18,19)20)22-10(9(8)15)13-2-5(11(16)24)1-6(3-13)12(17)25;/h2-3,7-10,14-15H,4H2,(H3-,16,17,18,19,20,24,25);/q;+1/p-2/t7-,8-,9-,10-;/m1./s1

> <INCHI_KEY>
GIEIRHLCPQGQDJ-WFFMJNDQSA-L

> <FORMULA>
C12H11NNiO9PS2

> <MOLECULAR_WEIGHT>
467.01

> <EXACT_MASS>
465.897176

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
34.98271822085766

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
lambda1-nickel(1+) ion {1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-5-(sulfanylcarbonyl)-2H-1lambda5-pyridin-1-ylium-3-carbonyl}sulfanide

> <JCHEM_LOGP>
-4.454085614471746

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.238875661973182

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2130540107908145

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7319665245238207

> <JCHEM_POLAR_SURFACE_AREA>
159.26

> <JCHEM_REFRACTIVITY>
98.9797

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
lambda1-nickel(1+) ion 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-5-(sulfanylcarbonyl)-2H-1lambda5-pyridin-1-ylium-3-carbonylsulfanide

> <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       1.650  -1.832   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.087  -0.748   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.929   0.820   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.846   3.846   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.182  -1.993   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.024  -0.426   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.381   3.370   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.136   4.275   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.890   3.370   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.366   1.905   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.808  -3.400   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.508  -0.265   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       3.460   0.659   0.000  0.00  0.00           N+1
HETATM   14  O   UNK     0       5.136   5.815   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.425   3.846   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       2.903  -4.646   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.134   1.142   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      10.931   1.826   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      11.920   3.767   0.000  0.00  0.00           O-1
HETATM   20  O   UNK     0       9.979   4.756   0.000  0.00  0.00           O-1
HETATM   21  O   UNK     0       8.990   2.815   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       5.906   1.905   0.000  0.00  0.00           O+0
HETATM   23  P   UNK     0      10.455   3.291   0.000  0.00  0.00           P+0
HETATM   24  S   UNK     0       5.339  -3.561   0.000  0.00  0.00           S+0
HETATM   25  S   UNK     0      -1.413  -1.511   0.000  0.00  0.00           S-1
HETATM   26 Ni   UNK     0      13.384   4.243   0.000  0.00  0.00          Ni+1
HETATM   27  H   UNK     0       6.622   4.891   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0       3.763   4.974   0.000  0.00  0.00           H+0
HETATM   29  H   UNK     0       2.801   2.281   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0       5.065   0.533   0.000  0.00  0.00           H+0
CONECT    1    5    6                                                       
CONECT    2    5   13                                                       
CONECT    3    6   13                                                       
CONECT    4    7   21                                                       
CONECT    5    1    2   11                                                  
CONECT    6    1    3   12                                                  
CONECT    7    4    8   22   27                                             
CONECT    8    7    9   14   28                                             
CONECT    9    8   10   15   29                                             
CONECT   10    9   13   22   30                                             
CONECT   11    5   16   24                                                  
CONECT   12    6   17   25                                                  
CONECT   13    2    3   10                                                  
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16   11                                                            
CONECT   17   12                                                            
CONECT   18   23                                                            
CONECT   19   23                                                            
CONECT   20   23                                                            
CONECT   21    4   23                                                       
CONECT   22    7   10                                                       
CONECT   23   18   19   20   21                                             
CONECT   24   11                                                            
CONECT   25   12                                                            
CONECT   27    7                                                            
CONECT   28    8                                                            
CONECT   29    9                                                            
CONECT   30   10                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   60    0
END

Synonyms

Value	Source
Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide	ChEBI
Ni(2+)-pyridinium-3,5-bisthiocarboxylate mononucleotide(1-)	ChEBI
Ni(II)-pyridinium-3,5-bisthiocarboxylic acid mononucleotide	Generator
Ni(2+)-pyridinium-3,5-bisthiocarboxylic acid mononucleotide(1-)	Generator
Ni(II)-pyridinium-3,5-bisthiocarboxylic acid mononucleotide(1-)	Generator

Molecular Formula

C₁₂H₁₁NNiO₉PS₂

Average Mass

467.01

Monoisotopic Mass

465.897176

IUPAC Name

lambda1-nickel(1+) ion {1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-5-(sulfanylcarbonyl)-2H-1lambda5-pyridin-1-ylium-3-carbonyl}sulfanide

Traditional Name

lambda1-nickel(1+) ion 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-5-(sulfanylcarbonyl)-2H-1lambda5-pyridin-1-ylium-3-carbonylsulfanide

CAS Registry Number

Not Available

SMILES

[Ni+].[H][C@]1(O)[C@@]([H])(O)[C@@]([H])(O[C@]1([H])COP([O-])([O-])=O)[N+]1=CC(=C=C([CH]1)C([S-])=O)C(S)=O

InChI Identifier

InChI=1S/C12H13NO9PS2.Ni/c14-8-7(4-21-23(18,19)20)22-10(9(8)15)13-2-5(11(16)24)1-6(3-13)12(17)25;/h2-3,7-10,14-15H,4H2,(H3-,16,17,18,19,20,24,25);/q;+1/p-2/t7-,8-,9-,10-;/m1./s1

InChI Key

GIEIRHLCPQGQDJ-WFFMJNDQSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Tetrahydrofuran
Secondary alcohol
Carbothioic s-acid
Carbodithioic acid
1,2-diol
Oxacycle
Azacycle
Organic transition metal salt
Organoheterocyclic compound
Thiocarboxylic acid or derivatives
Carboxylic acid derivative
Alkylthiol
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic salt
Organosulfur compound
Organonitrogen compound
Carbonyl group
Alcohol
Organic anion
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
logP	-4.5	ChemAxon
pKa (Strongest Acidic)	1.21	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	159.26 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	98.98 m³·mol⁻¹	ChemAxon
Polarizability	34.98 Å³	ChemAxon
Number of Rings	2	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

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0016758	Ni(II)-pyridinium-3,5-bisthiocarboxylic acid mononucleotide	Nickel	Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein		RHEA	34755880

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
Bacteria	Firmicutes	12	Human feces; Human
Bacteria	Verrucomicrobia	1	Human ; Human feces
Bacteria	Actinobacteria	4
Bacteria	Thermotogae	3

Exposure Sources

Source Type	Source Sub-type	Species	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

76962537

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

137373

Food Biomarker Ontology

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 Ni(II)-pyridinium-3,5-bisthiocarboxylic acid mononucleotide (MMDBc0056218)

MOL for #<Metabolite:0x00007fa508531240>

3D MOL for #<Metabolite:0x00007fa508531240>

3D SDF for #<Metabolite:0x00007fa508531240>

3D-SDF for #<Metabolite:0x00007fa508531240>

PDB for #<Metabolite:0x00007fa508531240>

3D PDB for #<Metabolite:0x00007fa508531240>

SMILES for #<Metabolite:0x00007fa508531240>

INCHI for #<Metabolite:0x00007fa508531240>

Structure for #<Metabolite:0x00007fa508531240>

3D Structure for #<Metabolite:0x00007fa508531240>