NP-MRD: Showing NP-Card for n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine (NP0204118)

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Record Information

Version

2.0

Created at

2022-09-04 23:44:03 UTC

Updated at

2022-09-04 23:44:03 UTC

NP-MRD ID

NP0204118

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine

Description

Streptidine belongs to the class of organic compounds known as cyclohexanols. Cyclohexanols are compounds containing an alcohol group attached to a cyclohexane ring. n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine is found in Streptomyces griseus. n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine was first documented in 2009 (PMID: 19764048). Based on a literature review a small amount of articles have been published on Streptidine (PMID: 27697730) (PMID: 22079046) (PMID: 21665399) (PMID: 22423580).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 36  0  0  0  0  0  0  0  0999 V2000
    3.2177    1.3434    1.6571 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3784    1.8878    0.7897 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1394    1.4242   -0.3944 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3708    2.1932   -1.5379 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6348    0.1133   -0.5163 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4752   -0.3460    0.2661 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4086    0.6740    0.1104 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5709    1.7428    1.0248 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9866    0.1634    0.3034 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9246    1.2212    0.1486 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3331    1.0833    0.2497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9762    0.7656    1.4665 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0685    1.2496   -0.7924 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7120    1.4846   -1.7378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1686   -0.9601   -0.6933 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5042   -1.3963   -0.5697 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2851   -2.0828   -0.2714 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3978   -3.0892   -1.2603 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1332   -1.7415   -0.0276 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6119   -2.6138    0.9829 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0911    1.9383   -2.2712 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8385    3.0803   -1.7415 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0682   -0.5718   -1.1653 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8331   -0.2863    1.3375 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4925    1.1692   -0.9019 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2820    1.3773    1.9008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0320   -0.2982    1.3120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5582    2.1817   -0.0564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6137    0.0427    2.0976 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8385    1.2800    1.7249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0299   -0.6296   -1.7322 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5399   -2.0709    0.1384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7497   -2.5438    0.6438 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4262   -3.6662   -1.2501 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7208   -2.0615   -0.9407 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0254   -2.0576    1.7062 H   0  0  0  0  0  0  0  0  0  0  0  0
 12 11  1  0
 11 13  2  0
 11 10  1  0
 10  9  1  0
  9 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 19  6  1  0
  6  5  1  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
 12 29  1  0
 12 30  1  0
 13 14  1  0
 10 28  1  0
  9 27  1  1
 15 31  1  6
 16 32  1  0
 17 33  1  1
 18 34  1  0
 19 35  1  6
 20 36  1  0
  6 24  1  1
  5 23  1  0
  4 21  1  0
  4 22  1  0
  2  1  1  0
  7 25  1  6
  8 26  1  0
M  END


  Mrv1652309052201442D          

 18 18  0  0  1  0            999 V2000
    0.0000    3.3000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   0  0  0  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    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  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
    0.0000    0.0000    0.0000 C   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
    0.0000    0.8250    0.0000 C   0  0  2  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  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  8 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
  5 17  1  0  0  0  0
 17 18  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0204118

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(=N)N[C@H]1[C@H](O)C(O)[C@H](O)[C@@H](NC(N)=N)C1O

> <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)/t1-,2+,3?,4+,5-,6?

> <INCHI_KEY>
MSXMXWJPFIDEMT-XGNJAFTASA-N

> <FORMULA>
C8H18N6O4

> <MOLECULAR_WEIGHT>
262.27

> <EXACT_MASS>
262.138953084

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
24.32976338569937

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(1R,3S,4R,6S)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine

> <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>
204.72

> <JCHEM_REFRACTIVITY>
80.5192

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
N-[(1R,3S,4R,6S)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  N   UNK     0       0.000   6.160   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -1.334   3.850   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       4.001  -0.770   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       5.335  -3.080   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       2.667  -3.080   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   17                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    8   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    5   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Value	Source
1,1'-(2,4,5,6-Tetrahydroxy-1,3-cyclohexylene)diguanidine	MeSH
Streptidine sulfate (1:1)	MeSH

Chemical Formula

C₈H₁₈N₆O₄

Average Mass

262.2700 Da

Monoisotopic Mass

262.13895 Da

IUPAC Name

N-[(1R,3S,4R,6S)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine

Traditional Name

N-[(1R,3S,4R,6S)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine

CAS Registry Number

Not Available

SMILES

NC(=N)N[C@H]1[C@H](O)C(O)[C@H](O)[C@@H](NC(N)=N)C1O

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)/t1-,2+,3?,4+,5-,6?

InChI Key

MSXMXWJPFIDEMT-XGNJAFTASA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces griseus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclohexanols. Cyclohexanols are compounds containing an alcohol group attached to a cyclohexane ring.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Cyclohexanols

Alternative Parents

Substituents

Cyclohexanol
Cyclitol or derivatives
Cyclic alcohol
Guanidine
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Polyol
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

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	10	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	204.72 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	80.52 m³·mol⁻¹	ChemAxon
Polarizability	24.33 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

388454

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439323

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Li Y, Su X, Peng Q, Qiao Y, Shi B: Method for determination of streptomycin and streptidine as markers for streptomycin industrial dregs monitoring in pig and poultry compound feeds. J Chromatogr B Analyt Technol Biomed Life Sci. 2016 Nov 1;1035:84-90. doi: 10.1016/j.jchromb.2016.09.037. Epub 2016 Sep 26. [PubMed:27697730 ]
Orgovan G, Noszal B: NMR analysis and site-specific protonation constants of streptomycin. J Pharm Biomed Anal. 2012 Feb 5;59:78-82. doi: 10.1016/j.jpba.2011.10.009. Epub 2011 Oct 18. [PubMed:22079046 ]
Holzgrabe U, Nap CJ, Kunz N, Almeling S: Identification and control of impurities in streptomycin sulfate by high-performance liquid chromatography coupled with mass detection and corona charged-aerosol detection. J Pharm Biomed Anal. 2011 Sep 10;56(2):271-9. doi: 10.1016/j.jpba.2011.05.027. Epub 2011 May 20. [PubMed:21665399 ]
Torres-Ruiz NM, Granados O, Meza G: Aminoglycosides: therapeutics, ototoxicity and hypersensitivity of mitochondrial genetic origin. Proc West Pharmacol Soc. 2011;54:49-51. [PubMed:22423580 ]
Pendela M, Hoogmartens J, Van Schepdael A, Adams E: LC-MS of streptomycin following desalting of a nonvolatile mobile phase and pH gradient. J Sep Sci. 2009 Oct;32(20):3418-24. doi: 10.1002/jssc.200900238. [PubMed:19764048 ]
LOTUS database [Link]

Showing NP-Card for n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine (NP0204118)

MOL for NP0204118 (n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine)

3D MOL for NP0204118 (n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine)

3D SDF for NP0204118 (n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine)

3D-SDF for NP0204118 (n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine)

PDB for NP0204118 (n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine)

3D PDB for NP0204118 (n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine)

SMILES for NP0204118 (n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine)

INCHI for NP0204118 (n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine)

Structure for NP0204118 (n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine)

3D Structure for NP0204118 (n-[(1r,3s,4r,6s)-3-carbamimidamido-2,4,5,6-tetrahydroxycyclohexyl]guanidine)