3D structure for N-{3-[4-(3-aminopropyl)piperazin-1-yl]propyl}-3-(alpha-D-galactopyranosyloxy)-5-nitrobenzamide (DB03235)

447977
  -OEChem-12201914093D

74 76  0     1  0  0  0  0  0999 V2000
   -0.7565   -1.8592   -0.1464 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0869   -1.5298    0.1022 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2290   -4.5589   -0.4775 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2903   -5.6483   -0.8844 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5994   -3.3175   -1.9477 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7099   -1.4347    2.3704 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9363    4.2440   -0.5769 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5640    3.2144    0.9185 O   0  5  0  0  0  0  0  0  0  0  0  0
   -7.1960    1.1155    1.0384 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9020    1.6470   -0.8341 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3591    0.3013   -0.1199 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3318    2.7178    0.1107 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.1983   -0.2854    0.6213 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3131    1.9870    0.8515 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.8270   -4.2338    0.4298 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1742   -4.3599   -0.2870 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6247   -2.7983    0.9322 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2982   -3.2887   -1.3706 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9934    0.1819   -0.8245 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2109    2.2398   -1.1347 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0501   -0.2924    0.1789 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2673    1.7665   -0.1304 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0341   -1.8981   -0.7878 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8952    2.0982   -1.7928 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3648   -0.1490    0.8405 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7540   -2.5874    1.5488 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4204    3.5078   -1.4357 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7668    0.0084    0.2493 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8075    3.5948   -0.0362 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8712   -0.4615    1.1986 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3841   -0.1968    0.1806 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3857    0.7538   -0.0314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6884    2.1131    0.0494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6470    3.1038   -0.1727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6852    0.2118    0.4735 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9878    1.5711    0.5542 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9894    2.5218    0.3421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7682   -4.9535    1.2533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0000   -4.2631    0.4281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3881   -2.5621    1.6849 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5859   -3.5051   -2.1760 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2332   -0.2015   -1.8257 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0277   -0.2480   -0.5321 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1674    3.3324   -1.0732 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5344    1.9834   -2.1529 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1126   -1.3857    0.1155 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7307   -0.0415    1.1996 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0192    2.1514    0.8684 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2203    2.2182   -0.4241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0069   -1.2125   -1.6460 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0239    1.4307   -1.7789 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2758    2.0759   -2.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2793    0.3773    1.7997 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2252   -1.2167    1.0559 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5216   -2.4356    0.7833 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0337   -3.4342    2.1834 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2343    4.2358   -1.5210 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6664    3.8083   -2.1746 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9639    1.0566   -0.0036 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8313   -0.5595   -0.6887 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3269   -3.8269   -1.1094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1901   -6.3081   -0.1771 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5333    3.3287    0.7389 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4869    4.6249    0.1548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6356   -2.6221   -2.6264 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7243   -1.5193    1.4438 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8172    0.1032    2.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1404    1.8031    0.5046 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5997   -1.3138    2.7434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3751    0.4501   -0.2719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4417   -0.5529    0.6335 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8976   -0.6644    1.2586 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2721   -0.8264   -0.2393 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2086    3.5852    0.4065 H   0  0  0  0  0  0  0  0  0  0  0  0
  1 17  1  0  0  0  0
  1 23  1  0  0  0  0
  2 23  1  0  0  0  0
  2 31  1  0  0  0  0
  3 15  1  0  0  0  0
  3 61  1  0  0  0  0
  4 16  1  0  0  0  0
  4 62  1  0  0  0  0
  5 18  1  0  0  0  0
  5 65  1  0  0  0  0
  6 26  1  0  0  0  0
  6 69  1  0  0  0  0
  7 34  2  0  0  0  0
  8 14  1  0  0  0  0
  9 14  2  0  0  0  0
 10 19  1  0  0  0  0
 10 20  1  0  0  0  0
 10 24  1  0  0  0  0
 11 21  1  0  0  0  0
 11 22  1  0  0  0  0
 11 25  1  0  0  0  0
 12 29  1  0  0  0  0
 12 34  1  0  0  0  0
 12 68  1  0  0  0  0
 13 30  1  0  0  0  0
 13 72  1  0  0  0  0
 13 73  1  0  0  0  0
 14 36  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 38  1  0  0  0  0
 16 18  1  0  0  0  0
 16 39  1  0  0  0  0
 17 26  1  0  0  0  0
 17 40  1  0  0  0  0
 18 23  1  0  0  0  0
 18 41  1  0  0  0  0
 19 21  1  0  0  0  0
 19 42  1  0  0  0  0
 19 43  1  0  0  0  0
 20 22  1  0  0  0  0
 20 44  1  0  0  0  0
 20 45  1  0  0  0  0
 21 46  1  0  0  0  0
 21 47  1  0  0  0  0
 22 48  1  0  0  0  0
 22 49  1  0  0  0  0
 23 50  1  0  0  0  0
 24 27  1  0  0  0  0
 24 51  1  0  0  0  0
 24 52  1  0  0  0  0
 25 28  1  0  0  0  0
 25 53  1  0  0  0  0
 25 54  1  0  0  0  0
 26 55  1  0  0  0  0
 26 56  1  0  0  0  0
 27 29  1  0  0  0  0
 27 57  1  0  0  0  0
 27 58  1  0  0  0  0
 28 30  1  0  0  0  0
 28 59  1  0  0  0  0
 28 60  1  0  0  0  0
 29 63  1  0  0  0  0
 29 64  1  0  0  0  0
 30 66  1  0  0  0  0
 30 67  1  0  0  0  0
 31 32  2  0  0  0  0
 31 35  1  0  0  0  0
 32 33  1  0  0  0  0
 32 70  1  0  0  0  0
 33 34  1  0  0  0  0
 33 37  2  0  0  0  0
 35 36  2  0  0  0  0
 35 71  1  0  0  0  0
 36 37  1  0  0  0  0
 37 74  1  0  0  0  0
M  CHG  2   8  -1  14   1
M  END
> <DATABASE_ID>
DB03235

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

> <ORIGINAL_SOURCE_URL>
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UEIGEWJJVQHIAX-MKQKURRLSA-N/SDF?record_type=3d

> <SMILES>
[H]N([H])CCCN1CCN(CCCN([H])C(=O)C2=CC(=CC(O[C@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)=C2)[N+]([O-])=O)CC1

> <INCHI_IDENTIFIER>
InChI=1S/C23H37N5O9/c24-3-1-5-26-7-9-27(10-8-26)6-2-4-25-22(33)15-11-16(28(34)35)13-17(12-15)36-23-21(32)20(31)19(30)18(14-29)37-23/h11-13,18-21,23,29-32H,1-10,14,24H2,(H,25,33)/t18-,19+,20+,21-,23+/m1/s1

> <INCHI_KEY>
UEIGEWJJVQHIAX-MKQKURRLSA-N

> <FORMULA>
C23H37N5O9

> <MOLECULAR_WEIGHT>
527.568

> <EXACT_MASS>
527.259127807

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_NEUTRAL_MICROSPECIES_CHARGE>
2.3103594724215606

> <JCHEM_AVERAGE_POLARIZABILITY>
55.58931376629645

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-{3-[4-(3-aminopropyl)piperazin-1-yl]propyl}-3-nitro-5-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzamide

> <ALOGPS_LOGP>
-0.30

> <JCHEM_LOGP>
-2.395387279

> <ALOGPS_LOGS>
-2.14

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NEUTRAL_CHARGE>
3

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
12.95316908863819

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.163508478605266

> <JCHEM_PKA_STRONGEST_BASIC>
9.875476241833946

> <JCHEM_POLAR_SURFACE_AREA>
204.12000000000003

> <JCHEM_REFRACTIVITY>
132.22869999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.81e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-{3-[4-(3-aminopropyl)piperazin-1-yl]propyl}-3-[2-(thiophen-2-yl)acetamido]-5-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzamide

> <JCHEM_VEBER_RULE>
0

$$$$

Similar Structures

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

3D structure for N-{3-[4-(3-aminopropyl)piperazin-1-yl]propyl}-3-(alpha-D-galactopyranosyloxy)-5-nitrobenzamide (DB03235)

Structure for N-{3-[4-(3-aminopropyl)piperazin-1-yl]propyl}-3-(alpha-D-galactopyranosyloxy)-5-nitrobenzamide (DB03235)