MiMeDB: Showing metabocard for gentamicin C1a (MMDBc0054494)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:15:38 UTC

Update Date

2022-08-12 20:09:00 UTC

MiMeDB ID

MMDBc0054494

Metabolite Identification

Common Name

gentamicin C1a

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231217522D          

 31 33  0  0  1  0            999 V2000
   -2.1434   -0.4125    0.0000 C   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
   -2.8579   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9597   -0.5091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1850   -0.5091    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0013   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.0013   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.4302   -5.3625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -5.3625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0013   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -6.6000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5724   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -6.6000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -5.3625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -7.4250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0013   -7.8375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5724   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  6  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  6  0  0  0
  6 12  1  1  0  0  0
 13 12  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  1  0  0  0
 17 19  1  0  0  0  0
 19 20  1  6  0  0  0
 21 20  1  1  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  6  0  0  0
 24 25  1  0  0  0  0
 23 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 21 28  1  0  0  0  0
 28 29  1  1  0  0  0
 19 30  1  0  0  0  0
 13 30  1  0  0  0  0
 30 31  1  1  0  0  0
M  END


  Mrv0541 02231217522D          

 31 33  0  0  1  0            999 V2000
   -2.1434   -0.4125    0.0000 C   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
   -2.8579   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9597   -0.5091    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1850   -0.5091    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0013   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.0013   -2.8875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.4302   -5.3625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -5.3625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0013   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -6.6000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5724   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -6.6000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -5.3625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -7.4250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0013   -7.8375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5724   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  6  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  6  0  0  0
  6 12  1  1  0  0  0
 13 12  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  1  0  0  0
 17 19  1  0  0  0  0
 19 20  1  6  0  0  0
 21 20  1  1  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  6  0  0  0
 24 25  1  0  0  0  0
 23 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 21 28  1  0  0  0  0
 28 29  1  1  0  0  0
 19 30  1  0  0  0  0
 13 30  1  0  0  0  0
 30 31  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054494

> <DATABASE_NAME>
MIME

> <SMILES>
CN[C@@H]1[C@@H](O)[C@@H](O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CN)CC[C@H]3N)[C@@H]2O)OC[C@]1(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C19H39N5O7/c1-19(27)7-28-18(13(26)16(19)24-2)31-15-11(23)5-10(22)14(12(15)25)30-17-9(21)4-3-8(6-20)29-17/h8-18,24-27H,3-7,20-23H2,1-2H3/t8-,9+,10-,11+,12-,13+,14+,15-,16+,17+,18+,19-/m0/s1

> <INCHI_KEY>
VEGXETMJINRLTH-BOZYPMBZSA-N

> <FORMULA>
C19H39N5O7

> <MOLECULAR_WEIGHT>
449.5423

> <EXACT_MASS>
449.284948627

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
47.460186634747295

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5R)-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,6S)-3-amino-6-(aminomethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

> <ALOGPS_LOGP>
-2.24

> <JCHEM_LOGP>
-3.9863109476666665

> <ALOGPS_LOGS>
-1.34

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
5

> <JCHEM_PKA>
13.15929624570665

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.548696465008678

> <JCHEM_PKA_STRONGEST_BASIC>
10.00379955057641

> <JCHEM_POLAR_SURFACE_AREA>
213.72

> <JCHEM_REFRACTIVITY>
108.8273

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gentamicin C1A

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -4.001  -2.310   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -8.002  -4.620   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -7.391  -0.950   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -5.945  -0.950   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -9.336  -5.390   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0     -10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0     -12.003 -10.010   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0      -9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -9.336 -11.550   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -8.002 -12.320   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -6.668 -11.550   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0      -4.001 -10.010   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0      -5.335 -13.860   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -6.668 -14.630   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -8.002 -13.860   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0      -9.336 -14.630   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0      -8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -6.668 -10.010   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    3   10   11                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    6   13                                                       
CONECT   13   12   14   30                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   30                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   28                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24                                                            
CONECT   26   23   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   21   29                                                  
CONECT   29   28                                                            
CONECT   30   19   13   31                                                  
CONECT   31   30                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

Synonyms

Not Available

Chemical Formula

C₁₉H₃₉N₅O₇

Average Molecular Weight

449.5423

Monoisotopic Molecular Weight

449.284948627

IUPAC Name

(2R,3R,4R,5R)-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,6S)-3-amino-6-(aminomethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

Traditional Name

gentamicin C1A

CAS Registry Number

Not Available

SMILES

CN[C@@H]1[C@@H](O)[C@@H](O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CN)CC[C@H]3N)[C@@H]2O)OC[C@]1(C)O

InChI Identifier

InChI=1S/C19H39N5O7/c1-19(27)7-28-18(13(26)16(19)24-2)31-15-11(23)5-10(22)14(12(15)25)30-17-9(21)4-3-8(6-20)29-17/h8-18,24-27H,3-7,20-23H2,1-2H3/t8-,9+,10-,11+,12-,13+,14+,15-,16+,17+,18+,19-/m0/s1

InChI Key

VEGXETMJINRLTH-BOZYPMBZSA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	20.5 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-4	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	10	ChemAxon
Physiological Charge	5	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	213.72 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	108.83 m³·mol⁻¹	ChemAxon
Polarizability	47.46 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_54) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0fef-0391800000-565efb1a33875acd2979	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-0941000000-44f407af52e186394247	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-006t-6920000000-895868370003cf3d22d8	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-2920100000-8b5976b06a47e86fe115	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01c9-0983400000-6a55feff705fe812e6c5	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0udi-2590000000-c9a8f682ee784b9f225e	2017-07-26	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum

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

Proteins

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Related Health Condition	Evidence Type	Measured in Matrix	Data Source	Reference

Microbial Sources

Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
	Proteobacteria	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference	Details

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

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 gentamicin C1a (MMDBc0054494)

MOL for #<Metabolite:0x000055b76dd0d4f8>

3D MOL for #<Metabolite:0x000055b76dd0d4f8>

3D SDF for #<Metabolite:0x000055b76dd0d4f8>

3D-SDF for #<Metabolite:0x000055b76dd0d4f8>

PDB for #<Metabolite:0x000055b76dd0d4f8>

3D PDB for #<Metabolite:0x000055b76dd0d4f8>

SMILES for #<Metabolite:0x000055b76dd0d4f8>

INCHI for #<Metabolite:0x000055b76dd0d4f8>

Structure for #<Metabolite:0x000055b76dd0d4f8>

3D Structure for #<Metabolite:0x000055b76dd0d4f8>