NP-MRD: Showing NP-Card for Kleboxymycin (NP0017042)

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Record Information

Version

2.0

Created at

2021-01-06 01:52:08 UTC

Updated at

2021-07-15 17:24:24 UTC

NP-MRD ID

NP0017042

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Kleboxymycin

Provided By

NPAtlas

Description

Kleboxymycin is found in Klebsiella oxytoca. Kleboxymycin was first documented in 2017 (PMID: 28972161). Based on a literature review very few articles have been published on (7S,8S)-8,11-dihydroxy-3,9-diazatricyclo[8.4.0.0³,⁷]Tetradeca-1(10),11,13-trien-2-one (PMID: 34142942) (PMID: 32126585).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242104203D          

 31 33  0  0  0  0            999 V2000
   -0.3536   -2.2725    1.5600 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2195   -1.1869    0.9563 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4683   -0.5495    0.4955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5870   -1.2040    0.9979 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8289   -0.7297    0.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9824    0.3637   -0.1641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8740    1.0458   -0.6873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0067    2.1207   -1.4950 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6339    0.5593   -0.3343 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.0029    1.1599    0.4274 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4598   -1.3182   -1.2480 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

 31 33  0  0  0  0  0  0  0  0999 V2000
   -0.3536   -2.2725    1.5600 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2195   -1.1869    0.9563 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4693    2.6537   -1.2431 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.1315   -0.2215    0.9883 H   0  0  0  0  0  0  0  0  0  0  0  0
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    2.0697   -2.0355    2.0295 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652306242104203D          

 31 33  0  0  0  0            999 V2000
   -0.3536   -2.2725    1.5600 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2195   -1.1869    0.9563 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4683   -0.5495    0.4955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5870   -1.2040    0.9979 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.6339    0.5593   -0.3343 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0017042

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C2N([H])[C@@]([H])(O[H])[C@@]3([H])N(C(=O)C2=C([H])C([H])=C1[H])C([H])([H])C([H])([H])C3([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C12H14N2O3/c15-9-5-1-3-7-10(9)13-11(16)8-4-2-6-14(8)12(7)17/h1,3,5,8,11,13,15-16H,2,4,6H2/t8-,11-/m0/s1

> <INCHI_KEY>
QEILHZZUMSPTRX-KWQFWETISA-N

> <FORMULA>
C12H14N2O3

> <MOLECULAR_WEIGHT>
234.255

> <EXACT_MASS>
234.100442319

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
23.970644640136705

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(7S,8S)-8,11-dihydroxy-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(14),10,12-trien-2-one

> <ALOGPS_LOGP>
0.42

> <JCHEM_LOGP>
1.020266699

> <ALOGPS_LOGS>
-0.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.266675949934642

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.443615461724965

> <JCHEM_PKA_STRONGEST_BASIC>
-0.2005159390819644

> <JCHEM_POLAR_SURFACE_AREA>
72.8

> <JCHEM_REFRACTIVITY>
63.3766

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.30e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(7S,8S)-8,11-dihydroxy-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(14),10,12-trien-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 31 33  0  0  0  0  0  0  0  0999 V2000
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   -0.2195   -1.1869    0.9563 C   0  0  0  0  0  0  0  0  0  0  0  0
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  8 21  1  0
 10 22  1  0
 11 23  1  6
 12 24  1  0
 13 25  1  1
 14 26  1  0
 14 27  1  0
 15 28  1  0
 15 29  1  0
 16 30  1  0
 16 31  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  O   UNK     0      -0.354  -2.272   1.560  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.220  -1.187   0.956  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.468  -0.550   0.496  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.587  -1.204   0.998  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.829  -0.730   0.655  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.982   0.364  -0.164  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.874   1.046  -0.687  0.00  0.00           C+0
HETATM    8  O   UNK     0      -3.007   2.121  -1.495  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.634   0.559  -0.334  0.00  0.00           C+0
HETATM   10  N   UNK     0      -0.547   1.299  -0.887  0.00  0.00           N+0
HETATM   11  C   UNK     0       0.736   0.802  -1.248  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.432   1.875  -1.861  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.592   0.290  -0.165  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.812  -0.451  -0.677  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.392  -0.971   0.641  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.191  -1.040   1.584  0.00  0.00           C+0
HETATM   17  N   UNK     0       1.070  -0.646   0.753  0.00  0.00           N+0
HETATM   18  H   UNK     0      -2.406  -2.048   1.629  0.00  0.00           H+0
HETATM   19  H   UNK     0      -4.710  -1.250   1.055  0.00  0.00           H+0
HETATM   20  H   UNK     0      -4.947   0.760  -0.452  0.00  0.00           H+0
HETATM   21  H   UNK     0      -2.391   2.714  -1.960  0.00  0.00           H+0
HETATM   22  H   UNK     0      -0.785   2.327  -1.016  0.00  0.00           H+0
HETATM   23  H   UNK     0       0.689   0.020  -2.057  0.00  0.00           H+0
HETATM   24  H   UNK     0       1.469   2.654  -1.243  0.00  0.00           H+0
HETATM   25  H   UNK     0       2.003   1.160   0.427  0.00  0.00           H+0
HETATM   26  H   UNK     0       2.460  -1.318  -1.248  0.00  0.00           H+0
HETATM   27  H   UNK     0       3.520   0.192  -1.208  0.00  0.00           H+0
HETATM   28  H   UNK     0       4.131  -0.222   0.988  0.00  0.00           H+0
HETATM   29  H   UNK     0       3.808  -1.980   0.537  0.00  0.00           H+0
HETATM   30  H   UNK     0       2.367  -0.277   2.393  0.00  0.00           H+0
HETATM   31  H   UNK     0       2.070  -2.035   2.030  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5   18                                                  
CONECT    5    4    6   19                                                  
CONECT    6    5    7   20                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7   21                                                       
CONECT    9    7   10    3                                                  
CONECT   10    9   11   22                                                  
CONECT   11   10   12   13   23                                             
CONECT   12   11   24                                                       
CONECT   13   11   14   17   25                                             
CONECT   14   13   15   26   27                                             
CONECT   15   14   16   28   29                                             
CONECT   16   15   17   30   31                                             
CONECT   17   16    2   13                                                  
CONECT   18    4                                                            
CONECT   19    5                                                            
CONECT   20    6                                                            
CONECT   21    8                                                            
CONECT   22   10                                                            
CONECT   23   11                                                            
CONECT   24   12                                                            
CONECT   25   13                                                            
CONECT   26   14                                                            
CONECT   27   14                                                            
CONECT   28   15                                                            
CONECT   29   15                                                            
CONECT   30   16                                                            
CONECT   31   16                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

RDKit          3D

31 33  0  0  0  0  0  0  0  0999 V2000
   -0.3536   -2.2725    1.5600 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2195   -1.1869    0.9563 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4683   -0.5495    0.4955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5870   -1.2040    0.9979 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8289   -0.7297    0.6548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9824    0.3637   -0.1641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8740    1.0458   -0.6873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0067    2.1207   -1.4950 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6339    0.5593   -0.3343 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5465    1.2990   -0.8869 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7360    0.8024   -1.2483 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4318    1.8749   -1.8608 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5916    0.2904   -0.1654 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8123   -0.4514   -0.6766 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3916   -0.9714    0.6414 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1912   -1.0399    1.5840 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0700   -0.6456    0.7532 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4063   -2.0479    1.6291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7104   -1.2504    1.0546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9466    0.7598   -0.4515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3914    2.7137   -1.9599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7852    2.3270   -1.0159 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6890    0.0196   -2.0569 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4693    2.6537   -1.2431 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0029    1.1599    0.4274 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4598   -1.3182   -1.2480 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5196    0.1922   -1.2079 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1315   -0.2215    0.9883 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8080   -1.9801    0.5372 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3666   -0.2773    2.3927 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0697   -2.0355    2.0295 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17  2  1  0
  9  3  1  0
 17 13  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  8 21  1  0
 10 22  1  0
 11 23  1  6
 12 24  1  0
 13 25  1  1
 14 26  1  0
 14 27  1  0
 15 28  1  0
 15 29  1  0
 16 30  1  0
 16 31  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₁₂H₁₄N₂O₃

Average Mass

234.2550 Da

Monoisotopic Mass

234.10044 Da

IUPAC Name

(7S,8S)-8,11-dihydroxy-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(14),10,12-trien-2-one

Traditional Name

(7S,8S)-8,11-dihydroxy-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(14),10,12-trien-2-one

CAS Registry Number

Not Available

SMILES

O[C@@H]1NC2=C(C=CC=C2O)C(=O)N2CCC[C@@H]12

InChI Identifier

InChI=1S/C12H14N2O3/c15-9-5-1-3-7-10(9)13-11(16)8-4-2-6-14(8)12(7)17/h1,3,5,8,11,13,15-16H,2,4,6H2/t8-,11-/m0/s1

InChI Key

QEILHZZUMSPTRX-KWQFWETISA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Klebsiella oxytoca	NPAtlas	28972161

Chemical Taxonomy

Classification

Not classified

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	0.42	ALOGPS
logP	1.02	ChemAxon
logS	-0.85	ALOGPS
pKa (Strongest Acidic)	9.44	ChemAxon
pKa (Strongest Basic)	-0.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	72.8 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	63.38 m³·mol⁻¹	ChemAxon
Polarizability	23.97 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA028467

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

146684602

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Tse H, Gu Q, Sze KH, Chu IK, Kao RY, Lee KC, Lam CW, Yang D, Tai SS, Ke Y, Chan E, Chan WM, Dai J, Leung SP, Leung SY, Yuen KY: A tricyclic pyrrolobenzodiazepine produced by Klebsiella oxytoca is associated with cytotoxicity in antibiotic-associated hemorrhagic colitis. J Biol Chem. 2017 Nov 24;292(47):19503-19520. doi: 10.1074/jbc.M117.791558. Epub 2017 Sep 26. [PubMed:28972161 ]
Shibu P, McCuaig F, McCartney AL, Kujawska M, Hall LJ, Hoyles L: Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster. Microb Genom. 2021 Jun;7(6). doi: 10.1099/mgen.0.000592. [PubMed:34142942 ]
Hubbard ATM, Newire E, Botelho J, Reine J, Wright E, Murphy EA, Hutton W, Roberts AP: Isolation of an antimicrobial-resistant, biofilm-forming, Klebsiella grimontii isolate from a reusable water bottle. Microbiologyopen. 2020 Jun;9(6):1128-1134. doi: 10.1002/mbo3.1023. Epub 2020 Mar 3. [PubMed:32126585 ]

Showing NP-Card for Kleboxymycin (NP0017042)

MOL for NP0017042 (Kleboxymycin)

3D MOL for NP0017042 (Kleboxymycin)

3D SDF for NP0017042 (Kleboxymycin)

3D-SDF for NP0017042 (Kleboxymycin)

PDB for NP0017042 (Kleboxymycin)

3D PDB for NP0017042 (Kleboxymycin)

SMILES for NP0017042 (Kleboxymycin)

INCHI for NP0017042 (Kleboxymycin)

Structure for NP0017042 (Kleboxymycin)

3D Structure for NP0017042 (Kleboxymycin)