NP-MRD: Showing NP-Card for Collismycin A (NP0022565)

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Record Information

Version

1.0

Created at

2021-01-06 07:44:18 UTC

Updated at

2021-07-15 17:39:23 UTC

NP-MRD ID

NP0022565

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Collismycin A

Provided By

NPAtlas

Description

Collismycin A is found in Streptomyces. It was first documented in 1994 (PMID: 7928696). Based on a literature review very few articles have been published on Collismycin B.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105363D          

 32 33  0  0  0  0            999 V2000
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    2.1709    2.0734   -0.5407 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3190    1.0092   -0.4147 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652306242105363D          

 32 33  0  0  0  0            999 V2000
    1.8284    3.4221   -0.5612 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1709    2.0734   -0.5407 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0022565

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O\N=C(/[H])C1=C(SC([H])([H])[H])C(OC([H])([H])[H])=C([H])C(=N1)C1=C([H])C([H])=C([H])C([H])=N1

> <INCHI_IDENTIFIER>
InChI=1S/C13H13N3O2S/c1-18-12-7-10(9-5-3-4-6-14-9)16-11(8-15-17)13(12)19-2/h3-8,17H,1-2H3/b15-8+

> <INCHI_KEY>
NQGMIPUYCWIEAW-OVCLIPMQSA-N

> <FORMULA>
C13H13N3O2S

> <MOLECULAR_WEIGHT>
275.33

> <EXACT_MASS>
275.072847845

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
29.304667170818977

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(E)-N-{[4-methoxy-5-(methylsulfanyl)-[2,2'-bipyridine]-6-yl]methylidene}hydroxylamine

> <ALOGPS_LOGP>
2.40

> <JCHEM_LOGP>
2.823898087666667

> <ALOGPS_LOGS>
-3.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.156272935645973

> <JCHEM_PKA_STRONGEST_BASIC>
2.963470435018815

> <JCHEM_POLAR_SURFACE_AREA>
67.60000000000001

> <JCHEM_REFRACTIVITY>
75.379

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.41e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(E)-N-{[4-methoxy-5-(methylsulfanyl)-[2,2'-bipyridine]-6-yl]methylidene}hydroxylamine

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 32 33  0  0  0  0  0  0  0  0999 V2000
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    4.1416   -1.4689    1.6280 H   0  0  0  0  0  0  0  0  0  0  0  0
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 17 18  1  0
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 17  3  1  0
 11  6  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  7 24  1  0
  8 25  1  0
  9 26  1  0
 10 27  1  0
 14 28  1  0
 16 29  1  0
 19 30  1  0
 19 31  1  0
 19 32  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  C   UNK     0       1.828   3.422  -0.561  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.171   2.073  -0.541  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.319   1.009  -0.415  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.053   1.117  -0.285  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.897   0.038  -0.159  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.337   0.152  -0.023  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.993   1.357  -0.007  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.390   1.418   0.127  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.124   0.257   0.245  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.423  -0.931   0.224  0.00  0.00           C+0
HETATM   11  N   UNK     0      -3.079  -0.958   0.094  0.00  0.00           N+0
HETATM   12  N   UNK     0      -0.302  -1.184  -0.168  0.00  0.00           N+0
HETATM   13  C   UNK     0       1.020  -1.364  -0.290  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.618  -2.709  -0.295  0.00  0.00           C+0
HETATM   15  N   UNK     0       0.809  -3.725  -0.175  0.00  0.00           N+0
HETATM   16  O   UNK     0       1.319  -4.986  -0.174  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.849  -0.264  -0.415  0.00  0.00           C+0
HETATM   18  S   UNK     0       3.608  -0.524  -0.577  0.00  0.00           S+0
HETATM   19  C   UNK     0       4.417  -0.541   1.048  0.00  0.00           C+0
HETATM   20  H   UNK     0       2.149   3.892   0.413  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.794   3.651  -0.809  0.00  0.00           H+0
HETATM   22  H   UNK     0       2.495   3.918  -1.325  0.00  0.00           H+0
HETATM   23  H   UNK     0      -0.446   2.119  -0.287  0.00  0.00           H+0
HETATM   24  H   UNK     0      -2.438   2.283  -0.099  0.00  0.00           H+0
HETATM   25  H   UNK     0      -4.914   2.365   0.140  0.00  0.00           H+0
HETATM   26  H   UNK     0      -6.207   0.243   0.351  0.00  0.00           H+0
HETATM   27  H   UNK     0      -5.008  -1.847   0.318  0.00  0.00           H+0
HETATM   28  H   UNK     0       2.673  -2.826  -0.393  0.00  0.00           H+0
HETATM   29  H   UNK     0       0.664  -5.758  -0.094  0.00  0.00           H+0
HETATM   30  H   UNK     0       5.510  -0.599   0.876  0.00  0.00           H+0
HETATM   31  H   UNK     0       4.226   0.369   1.630  0.00  0.00           H+0
HETATM   32  H   UNK     0       4.142  -1.469   1.628  0.00  0.00           H+0
CONECT    1    2   20   21   22                                             
CONECT    2    1    3                                                       
CONECT    3    2    4   17                                                  
CONECT    4    3    5   23                                                  
CONECT    5    4    6   12                                                  
CONECT    6    5    7   11                                                  
CONECT    7    6    8   24                                                  
CONECT    8    7    9   25                                                  
CONECT    9    8   10   26                                                  
CONECT   10    9   11   27                                                  
CONECT   11   10    6                                                       
CONECT   12    5   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13   15   28                                                  
CONECT   15   14   16                                                       
CONECT   16   15   29                                                       
CONECT   17   13   18    3                                                  
CONECT   18   17   19                                                       
CONECT   19   18   30   31   32                                             
CONECT   20    1                                                            
CONECT   21    1                                                            
CONECT   22    1                                                            
CONECT   23    4                                                            
CONECT   24    7                                                            
CONECT   25    8                                                            
CONECT   26    9                                                            
CONECT   27   10                                                            
CONECT   28   14                                                            
CONECT   29   16                                                            
CONECT   30   19                                                            
CONECT   31   19                                                            
CONECT   32   19                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   66    0
END

RDKit          3D

32 33  0  0  0  0  0  0  0  0999 V2000
    1.8284    3.4221   -0.5612 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1709    2.0734   -0.5407 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3190    1.0092   -0.4147 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0525    1.1169   -0.2850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8965    0.0382   -0.1593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3368    0.1518   -0.0232 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9930    1.3568   -0.0074 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3901    1.4179    0.1265 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1241    0.2567    0.2448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4226   -0.9309    0.2240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0790   -0.9578    0.0938 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3022   -1.1837   -0.1683 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0195   -1.3639   -0.2903 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6178   -2.7093   -0.2947 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8085   -3.7250   -0.1749 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3186   -4.9862   -0.1741 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8489   -0.2636   -0.4154 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6083   -0.5240   -0.5769 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.4171   -0.5407    1.0484 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1489    3.8919    0.4129 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7943    3.6513   -0.8090 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4946    3.9176   -1.3253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4459    2.1195   -0.2868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4377    2.2834   -0.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9139    2.3651    0.1396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2072    0.2430    0.3511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0078   -1.8469    0.3179 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6734   -2.8259   -0.3930 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6642   -5.7579   -0.0939 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5098   -0.5989    0.8756 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2256    0.3687    1.6303 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1416   -1.4689    1.6280 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
  5 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 13 17  2  0
 17 18  1  0
 18 19  1  0
 17  3  1  0
 11  6  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  7 24  1  0
  8 25  1  0
  9 26  1  0
 10 27  1  0
 14 28  1  0
 16 29  1  0
 19 30  1  0
 19 31  1  0
 19 32  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Collismycin a	MeSH
(e)-N-{[4-methoxy-5-(methylsulphanyl)-[2,2'-bipyridine]-6-yl]methylidene}hydroxylamine	Generator

Chemical Formula

C₁₃H₁₃N₃O₂S

Average Mass

275.3300 Da

Monoisotopic Mass

275.07285 Da

IUPAC Name

(E)-N-{[4-methoxy-5-(methylsulfanyl)-[2,2'-bipyridine]-6-yl]methylidene}hydroxylamine

Traditional Name

(E)-N-{[4-methoxy-5-(methylsulfanyl)-[2,2'-bipyridine]-6-yl]methylidene}hydroxylamine

CAS Registry Number

Not Available

SMILES

COC1=CC(=NC(\C=N\O)=C1SC)C1=CC=CC=N1

InChI Identifier

InChI=1S/C13H13N3O2S/c1-18-12-7-10(9-5-3-4-6-14-9)16-11(8-15-17)13(12)19-2/h3-8,17H,1-2H3/b15-8+

InChI Key

NQGMIPUYCWIEAW-OVCLIPMQSA-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
Streptomyces	NPAtlas	7928696

Species Where Detected

Species Name	Source	Reference
Streptomyces sp. MQ22	KNApSAcK Database	22123792

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	2.4	ALOGPS
logP	2.82	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	8.16	ChemAxon
pKa (Strongest Basic)	2.96	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	67.6 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	75.38 m³·mol⁻¹	ChemAxon
Polarizability	29.3 Å³	ChemAxon
Number of Rings	2	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

NPA020595

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00016674

Chemspider ID

20130229

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

135482271

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Shindo K, Yamagishi Y, Okada Y, Kawai H: Collismycins A and B, novel non-steroidal inhibitors of dexamethasone-glucocorticoid receptor binding. J Antibiot (Tokyo). 1994 Sep;47(9):1072-4. doi: 10.7164/antibiotics.47.1072. [PubMed:7928696 ]

Showing NP-Card for Collismycin A (NP0022565)

MOL for NP0022565 (Collismycin A)

3D MOL for NP0022565 (Collismycin A)

3D SDF for NP0022565 (Collismycin A)

3D-SDF for NP0022565 (Collismycin A)

PDB for NP0022565 (Collismycin A)

3D PDB for NP0022565 (Collismycin A)

SMILES for NP0022565 (Collismycin A)

INCHI for NP0022565 (Collismycin A)

Structure for NP0022565 (Collismycin A)

3D Structure for NP0022565 (Collismycin A)