NP-MRD: Showing NP-Card for Congocidine (NP0062219)

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Record Information

Version

2.0

Created at

2022-04-28 06:53:10 UTC

Updated at

2022-04-28 06:53:10 UTC

NP-MRD ID

NP0062219

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Congocidine

Description

Netropsin, also known as congocidine or sinanomycin, belongs to the class of organic compounds known as alpha amino acid amides. These are amide derivatives of alpha amino acids. Crystallographic structures of DNA-bound Netropsin have been obtained and elucidate details of how the drug binds in the minor groove. Netropsin binds to the minor groove of AT-rich sequences of double stranded DNA. Netropsin is a very strong basic compound (based on its pKa). Netropsin (also termed congocidine or sinanomycin) is a polyamide with antibiotic and antiviral activity. Thus, it removes supercoils when interacting with positively supercoiled DNA and introduces (additional) negative supercoils when binding to relaxed or negatively supercoiled DNA. In contrast, netropsin does not bind single stranded DNA or double stranded RNA. Netropsin's effect on supercoiled DNA was observed in detail on single molecules using a magnetic tweezers. In the bound structure, the drug makes hydrogen bonding interactions with four subsequent base pairs of the DNA duplex, locally displacing the water molecules of the spine of hydration. Netropsin was discovered by Finlay et al., And first isolated from the actinobacterium Streptomyces netropsis. It has been shown that Netropsin is active both against Gram-positive bacteria and Gram-negative bacteria. Congocidine is found in Streptomyces achromogenes, Streptomyces netropsis and Streptomyces sp. No.7618. Using gel mobility and analytical ultracentrifugation, it was shown that Netropsin binding to DNA increases the twist per base by similar to 9˚ per molecule bound.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 05041408422D          

 31 32  0  0  0  0            999 V2000
   -0.8551   -0.4751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0446    0.1260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760    0.8974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7615    1.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0766    2.2605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1356    1.2330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8944    2.9381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9698    1.2685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2751   -0.0946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8836    2.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6876    0.6199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819    0.8974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6641    1.5460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904    1.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2813    2.3861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674    1.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8437    1.4598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2921    3.2352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9049    0.8974    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904    2.1349    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0768    2.9803    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1206    4.0422    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    0.8974    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6790    2.6832    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4967    2.6410    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5081    0.7061    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4681    0.0769    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2162    0.9329    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4529    1.5791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674    2.1349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3587    2.1272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
 10  5  1  0  0  0  0
 10  8  2  0  0  0  0
 11  6  1  0  0  0  0
 11  9  2  0  0  0  0
 12  6  2  0  0  0  0
 13  5  2  0  0  0  0
 14  3  1  0  0  0  0
 15  7  1  0  0  0  0
 16 12  1  0  0  0  0
 17 13  1  0  0  0  0
 19 14  2  0  0  0  0
 20 14  1  0  0  0  0
 21 18  2  0  0  0  0
 22 18  1  0  0  0  0
 23  4  1  0  0  0  0
 23 16  1  0  0  0  0
 24  7  1  0  0  0  0
 24 18  1  0  0  0  0
 25 10  1  4  0  0  0
 25 15  2  0  0  0  0
 26 11  1  0  0  0  0
 26 17  1  0  0  0  0
 27  1  1  0  0  0  0
 27  9  1  0  0  0  0
 27 12  1  0  0  0  0
 28  2  1  0  0  0  0
 28  8  1  0  0  0  0
 28 13  1  0  0  0  0
 29 15  1  0  0  0  0
 30 16  2  0  0  0  0
 31 17  2  0  0  0  0
M  END

     RDKit          3D

 57 58  0  0  0  0  0  0  0  0999 V2000
   -9.1497    0.1714   -1.1701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8742    0.2833   -0.1852 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9768    1.1227    0.1901 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3310    1.9615   -0.7521 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6363    1.2279    1.5927 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8159    0.1661    2.2282 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5206   -0.0773    1.7061 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1563   -0.5718    0.4477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0584   -0.8636   -0.3683 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7711   -0.7558    0.0729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6405   -0.4512    0.8103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5089   -0.7988    0.0904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1620   -0.6255    0.5864 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9632   -1.0529   -0.0934 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7749   -1.6191   -1.2284 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3253   -0.9239    0.3540 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4234   -1.3184   -0.4400 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5487   -1.0899    0.2996 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8974   -1.3388   -0.0261 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.7061   -0.5285   -0.5678 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9919   -0.9618   -0.8007 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3035    0.8367   -0.9406 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8856    1.1979   -2.2012 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.3117    1.4271   -2.2763 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7034    2.7155   -1.7477 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.0895    0.6228   -2.7177 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.1299   -0.2921   -3.1149 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1326   -0.5587    1.5329 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7835   -0.4743    1.5262 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0749    0.0334    2.6777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9822   -1.3109   -1.0790 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3340   -1.2831   -1.0842 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1487   -1.7456   -2.1645 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5039    1.6381   -1.2626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6859    2.9195   -0.9399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1172    2.2111    1.8187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5953    1.2822    2.2035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4073   -0.8045    2.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7245    0.4431    3.3139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7045    0.1510    2.3607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6646    0.0052    1.8118 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0471   -0.1431    1.5093 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3708   -1.7245   -1.4579 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2927   -1.9243   -0.7374 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5310    1.5694   -0.1244 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1826    0.8352   -0.9962 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3456    1.3062   -3.0533 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8582    3.5147   -2.3531 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7947    2.7706   -0.7233 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8060   -0.2816    2.3179 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8275    0.2155    3.5277 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3862   -0.6813    3.1332 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6285    1.0183    2.4755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3661   -1.6838   -1.8862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5415   -2.1138   -3.0159 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8949   -1.0103   -2.5162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7499   -2.6373   -1.8370 H   0  0  0  0  0  0  0  0  0  0  0  0
 33 32  1  0
 32 31  1  0
 31 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  2  0
 17 18  1  0
 18 28  2  0
 28 29  1  0
 29 30  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 24 26  2  0
 12 11  1  0
 11 10  2  0
 10  8  1  0
  8  9  2  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
 10 32  1  0
 29 16  1  0
 33 55  1  0
 33 56  1  0
 33 57  1  0
 31 54  1  0
 13 42  1  0
 17 43  1  0
 28 50  1  0
 30 51  1  0
 30 52  1  0
 30 53  1  0
 21 44  1  0
 22 45  1  0
 22 46  1  0
 23 47  1  0
 25 48  1  0
 25 49  1  0
 26 27  1  0
 11 41  1  0
  7 40  1  0
  6 38  1  0
  6 39  1  0
  5 36  1  0
  5 37  1  0
  4 34  1  0
  4 35  1  0
  2  1  1  0
M  END


  Mrv0541 05041408422D          

 31 32  0  0  0  0            999 V2000
   -0.8551   -0.4751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0446    0.1260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760    0.8974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7615    1.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0766    2.2605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1356    1.2330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8944    2.9381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9698    1.2685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2751   -0.0946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8836    2.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6876    0.6199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819    0.8974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6641    1.5460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904    1.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2813    2.3861    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674    1.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8437    1.4598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2921    3.2352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9049    0.8974    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1904    2.1349    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0768    2.9803    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1206    4.0422    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    0.8974    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6790    2.6832    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4967    2.6410    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5081    0.7061    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4681    0.0769    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2162    0.9329    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4529    1.5791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674    2.1349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3587    2.1272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
 10  5  1  0  0  0  0
 10  8  2  0  0  0  0
 11  6  1  0  0  0  0
 11  9  2  0  0  0  0
 12  6  2  0  0  0  0
 13  5  2  0  0  0  0
 14  3  1  0  0  0  0
 15  7  1  0  0  0  0
 16 12  1  0  0  0  0
 17 13  1  0  0  0  0
 19 14  2  0  0  0  0
 20 14  1  0  0  0  0
 21 18  2  0  0  0  0
 22 18  1  0  0  0  0
 23  4  1  0  0  0  0
 23 16  1  0  0  0  0
 24  7  1  0  0  0  0
 24 18  1  0  0  0  0
 25 10  1  4  0  0  0
 25 15  2  0  0  0  0
 26 11  1  0  0  0  0
 26 17  1  0  0  0  0
 27  1  1  0  0  0  0
 27  9  1  0  0  0  0
 27 12  1  0  0  0  0
 28  2  1  0  0  0  0
 28  8  1  0  0  0  0
 28 13  1  0  0  0  0
 29 15  1  0  0  0  0
 30 16  2  0  0  0  0
 31 17  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0062219

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C=C(NC(=O)C2=CC(=CN2C)N=C(O)CNC(N)=N)C=C1C(=O)NCCC(N)=N

> <INCHI_IDENTIFIER>
InChI=1S/C18H26N10O3/c1-27-9-11(6-12(27)16(30)23-4-3-14(19)20)26-17(31)13-5-10(8-28(13)2)25-15(29)7-24-18(21)22/h5-6,8-9H,3-4,7H2,1-2H3,(H3,19,20)(H,23,30)(H,25,29)(H,26,31)(H4,21,22,24)

> <INCHI_KEY>
IDBIFFKSXLYUOT-UHFFFAOYSA-N

> <FORMULA>
C18H26N10O3

> <MOLECULAR_WEIGHT>
430.4642

> <EXACT_MASS>
430.218934748

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
45.947599598546084

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-carbamimidamido-N-[5-({5-[(2-carbamimidoylethyl)carbamoyl]-1-methyl-1H-pyrrol-3-yl}carbamoyl)-1-methyl-1H-pyrrol-3-yl]ethanimidic acid

> <ALOGPS_LOGP>
-0.28

> <JCHEM_LOGP>
-3.6565417763087384

> <ALOGPS_LOGS>
-3.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
13.040446392977998

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.407363503097484

> <JCHEM_PKA_STRONGEST_BASIC>
12.440667567035302

> <JCHEM_POLAR_SURFACE_AREA>
212.42

> <JCHEM_REFRACTIVITY>
139.52530000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.03e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-carbamimidamido-N-[5-({5-[(2-carbamimidoylethyl)carbamoyl]-1-methylpyrrol-3-yl}carbamoyl)-1-methylpyrrol-3-yl]ethanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   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       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   24  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   25  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   26  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   27  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   28  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   29  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1   27                                                            
CONECT    2   28                                                            
CONECT    3    4   14                                                       
CONECT    4    3   23                                                       
CONECT    5   10   13                                                       
CONECT    6   11   12                                                       
CONECT    7   15   24                                                       
CONECT    8   10   28                                                       
CONECT    9   11   27                                                       
CONECT   10    5    8   25                                                  
CONECT   11    6    9   26                                                  
CONECT   12    6   16   27                                                  
CONECT   13    5   17   28                                                  
CONECT   14    3   19   20                                                  
CONECT   15    7   25   29                                                  
CONECT   16   12   23   30                                                  
CONECT   17   13   26   31                                                  
CONECT   18   21   22   24                                                  
CONECT   19   14                                                            
CONECT   20   14                                                            
CONECT   21   18                                                            
CONECT   22   18                                                            
CONECT   23    4   16                                                       
CONECT   24    7   18                                                       
CONECT   25   10   15                                                       
CONECT   26   11   17                                                       
CONECT   27    1    9   12                                                  
CONECT   28    2    8   13                                                  
CONECT   29   15                                                            
CONECT   30   16                                                            
CONECT   31   17                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   64    0
END

View in JSmol

Synonyms

Value	Source
Hydrochloride, netropsin	MeSH
Congocidine	MeSH
Netropsin hydrochloride	MeSH
Sinanomycin	MeSH
2-Carbamimidamido-N-[5-({5-[(2-carbamimidoylethyl)carbamoyl]-1-methyl-1H-pyrrol-3-yl}carbamoyl)-1-methyl-1H-pyrrol-3-yl]ethanimidate	Generator

Chemical Formula

C₁₈H₂₆N₁₀O₃

Average Mass

430.4642 Da

Monoisotopic Mass

430.21893 Da

IUPAC Name

2-carbamimidamido-N-[5-({5-[(2-carbamimidoylethyl)carbamoyl]-1-methyl-1H-pyrrol-3-yl}carbamoyl)-1-methyl-1H-pyrrol-3-yl]ethanimidic acid

Traditional Name

2-carbamimidamido-N-[5-({5-[(2-carbamimidoylethyl)carbamoyl]-1-methylpyrrol-3-yl}carbamoyl)-1-methylpyrrol-3-yl]ethanimidic acid

CAS Registry Number

Not Available

SMILES

CN1C=C(NC(=O)C2=CC(=CN2C)N=C(O)CNC(N)=N)C=C1C(=O)NCCC(N)=N

InChI Identifier

InChI=1S/C18H26N10O3/c1-27-9-11(6-12(27)16(30)23-4-3-14(19)20)26-17(31)13-5-10(8-28(13)2)25-15(29)7-24-18(21)22/h5-6,8-9H,3-4,7H2,1-2H3,(H3,19,20)(H,23,30)(H,25,29)(H,26,31)(H4,21,22,24)

InChI Key

IDBIFFKSXLYUOT-UHFFFAOYSA-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 achromogenes	LOTUS Database	35616633
Streptomyces netropsis	LOTUS Database	35616633
Streptomyces sp. No.7618	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acid amides. These are amide derivatives of alpha amino acids.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acid amides

Alternative Parents

Substituents

Alpha-amino acid amide
2-heteroaryl carboxamide
Pyrrole-2-carboxamide
Pyrrole-2-carboxylic acid or derivatives
N-arylamide
N-methylpyrrole
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Carboxamide group
Guanidine
Secondary carboxylic acid amide
Azacycle
Carboxylic acid amidine
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Amidine
Carboximidamide
Organonitrogen compound
Organic nitrogen compound
Organooxygen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	-0.28	ALOGPS
logP	-3.7	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	5.41	ChemAxon
pKa (Strongest Basic)	12.44	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	212.42 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	139.53 m³·mol⁻¹	ChemAxon
Polarizability	45.95 Å³	ChemAxon
Number of Rings	2	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Netropsin

METLIN ID

Not Available

PubChem Compound

4461

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Congocidine (NP0062219)

MOL for NP0062219 (Congocidine)

3D MOL for NP0062219 (Congocidine)

3D SDF for NP0062219 (Congocidine)

3D-SDF for NP0062219 (Congocidine)

PDB for NP0062219 (Congocidine)

3D PDB for NP0062219 (Congocidine)

SMILES for NP0062219 (Congocidine)

INCHI for NP0062219 (Congocidine)

Structure for NP0062219 (Congocidine)

3D Structure for NP0062219 (Congocidine)