MiMeDB: Showing metabocard for streptidine (MMDBc0056317)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:22:41 UTC

Update Date

2025-10-07 16:04:20 UTC

Metabolite ID

MMDBc0056317

Metabolite Identification

Common Name

streptidine

Description

Streptidine is a member of the aminoglycoside class of antibiotics, primarily known as a metabolite of streptomycin. Its chemical structure includes a guanidino group, which plays a crucial role in its interaction with biological systems. Streptidine is involved in various biochemical pathways, notably in the context of antibiotic activity and resistance mechanisms. For instance, it acts as a "decoy acceptor" for the aminoglycoside-inactivating enzyme adenyl transferase, thereby rescuing the antibiotic activity of streptomycin against resistant strains of Escherichia coli (PMID:17609790 ). Additionally, streptidine has been detected in blood samples from elderly patients, indicating its metabolic relevance (PMID:22423580 ). Analytical methods have been developed for the simultaneous determination of streptomycin and streptidine in compound feeds, emphasizing its importance in monitoring antibiotic residues (PMID:27697730 ). Furthermore, studies involving NMR-pH titrations have provided insights into the proton-binding processes of streptidine, contributing to the understanding of its chemical behavior (PMID:22079046 ). Overall, streptidine's structural characteristics and its role in antibiotic activity highlight its significance in both chemistry and microbiology.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222222D          

 24 24  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  9  7  2  0  0  0  0
 10  7  1  0  0  0  0
 11  8  2  0  0  0  0
 12  8  1  0  0  0  0
  1 13  1  6  0  0  0
 13  7  1  0  0  0  0
  2 14  1  6  0  0  0
 14  8  1  0  0  0  0
  3 15  1  6  0  0  0
  4 16  1  1  0  0  0
  5 17  1  1  0  0  0
  6 18  1  6  0  0  0
  1 19  1  1  0  0  0
  2 20  1  1  0  0  0
  3 21  1  6  0  0  0
  4 22  1  6  0  0  0
  5 23  1  6  0  0  0
  6 24  1  1  0  0  0
M  CHG  2   9   1  10   1
M  END
> <DATABASE_ID>
MMDBc0056317

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(O)[C@@]([H])(O)[C@]([H])(NC(N)=N)[C@@]([H])(O)[C@]([H])(NC([NH3+])=[NH2+])[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C8H18N6O4/c9-7(10)13-1-3(15)2(14-8(11)12)5(17)6(18)4(1)16/h1-6,15-18H,(H4,9,10,13)(H4,11,12,14)/p+2/t1-,2+,3-,4+,5-,6-

> <INCHI_KEY>
MSXMXWJPFIDEMT-FAEUDGQSSA-P

> <FORMULA>
C8H20N6O4

> <MOLECULAR_WEIGHT>
264.285

> <EXACT_MASS>
264.153505988

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
25.856397257485682

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[azaniumyl({[(1S,2R,3R,4S,5R,6R)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]amino})methylidene]azanium

> <JCHEM_LOGP>
-4.845562451149027

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
14.431414874012066

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.970313279366138

> <JCHEM_PKA_STRONGEST_BASIC>
11.525146567361201

> <JCHEM_POLAR_SURFACE_AREA>
208.07999999999998

> <JCHEM_REFRACTIVITY>
92.612

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[ammonio({[(1S,2R,3R,4S,5R,6R)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]amino})methylidene]azanium

> <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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       6.668   2.310   0.000  0.00  0.00           N+1
HETATM   10  N   UNK     0       5.335  -0.000   0.000  0.00  0.00           N+1
HETATM   11  N   UNK     0      -2.667   4.620   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   4.620   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       4.001   2.310   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0      -1.334   2.310   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       2.667   3.080   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   3.080   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       2.667  -1.540   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0      -0.000  -1.540   0.000  0.00  0.00           H+0
CONECT    1    3    4   13   19                                             
CONECT    2    3    5   14   20                                             
CONECT    3    1    2   15   21                                             
CONECT    4    1    6   16   22                                             
CONECT    5    2    6   17   23                                             
CONECT    6    4    5   18   24                                             
CONECT    7    9   10   13                                                  
CONECT    8   11   12   14                                                  
CONECT    9    7                                                            
CONECT   10    7                                                            
CONECT   11    8                                                            
CONECT   12    8                                                            
CONECT   13    1    7                                                       
CONECT   14    2    8                                                       
CONECT   15    3                                                            
CONECT   16    4                                                            
CONECT   17    5                                                            
CONECT   18    6                                                            
CONECT   19    1                                                            
CONECT   20    2                                                            
CONECT   21    3                                                            
CONECT   22    4                                                            
CONECT   23    5                                                            
CONECT   24    6                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END

Synonyms

Value	Source
Streptidine	ChEBI
Streptidine dication	ChEBI
{[(1R,2S,3S,4R,5R,6S)-2,4,5,6-tetrahydroxycyclohexane-1,3-diyl]diazanediyl}bis(aminomethaniminium)	ChEBI

Molecular Formula

C₈H₂₀N₆O₄

Average Mass

264.285

Monoisotopic Mass

264.153505988

IUPAC Name

[azaniumyl({[(1S,2R,3R,4S,5R,6R)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]amino})methylidene]azanium

Traditional Name

[ammonio({[(1S,2R,3R,4S,5R,6R)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]amino})methylidene]azanium

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O)[C@@]([H])(O)[C@]([H])(NC(N)=N)[C@@]([H])(O)[C@]([H])(NC([NH3+])=[NH2+])[C@@]1([H])O

InChI Identifier

InChI=1S/C8H18N6O4/c9-7(10)13-1-3(15)2(14-8(11)12)5(17)6(18)4(1)16/h1-6,15-18H,(H4,9,10,13)(H4,11,12,14)/p+2/t1-,2+,3-,4+,5-,6-

InChI Key

MSXMXWJPFIDEMT-FAEUDGQSSA-P

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-4.8	ChemAxon
pKa (Strongest Acidic)	12.97	ChemAxon
pKa (Strongest Basic)	11.53	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	208.08 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	92.61 m³·mol⁻¹	ChemAxon
Polarizability	25.86 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	Firmicutes	1	Human feces

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

24726442

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

184376

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 streptidine (MMDBc0056317)

MOL for #<Metabolite:0x0000561536995d58>

3D MOL for #<Metabolite:0x0000561536995d58>

3D SDF for #<Metabolite:0x0000561536995d58>

3D-SDF for #<Metabolite:0x0000561536995d58>

PDB for #<Metabolite:0x0000561536995d58>

3D PDB for #<Metabolite:0x0000561536995d58>

SMILES for #<Metabolite:0x0000561536995d58>

INCHI for #<Metabolite:0x0000561536995d58>

Structure for #<Metabolite:0x0000561536995d58>

3D Structure for #<Metabolite:0x0000561536995d58>