3D structure for N-{3-[4-(3-amino-propyl)-piperazin-1-yl]-propyl}-3-nitro-5-(galactopyranosyl)-beta-benzamide (DB04073)

447976
  -OEChem-12051918303D

74 76  0     1  0  0  0  0  0999 V2000
   -2.4743   -0.1987   -1.4837 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8188    2.0104   -1.1107 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1744   -0.6804   -2.2812 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2836    0.6159   -0.0860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0823    2.3751    0.5664 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6597   -3.0303   -1.6964 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6543    0.7020   -3.1738 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7919    3.5948    2.2794 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.6877    4.1040    2.6431 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7108   -1.7934    0.1241 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4212   -2.0571    1.8695 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9955    0.4522   -1.2989 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2384   -3.0099    3.1707 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5796    3.5463    1.9595 N   0  3  0  0  0  0  0  0  0  0  0  0
   -4.7082   -0.9992   -0.9684 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.9215    0.1993   -0.0434 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.2158   -1.3412   -1.0382 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.0249    1.3700   -0.4457 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4816   -2.4575   -0.3266 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8720   -1.9448    1.5753 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2600   -1.9078    0.4180 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6510   -1.3939    2.3199 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5720    0.9133   -0.5948 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8752   -2.3198   -0.5852 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2571   -1.5289    2.5782 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9262   -2.4791   -2.0100 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9585   -1.7124   -1.9868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8976   -2.5304    2.5166 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1035   -0.1891   -1.9697 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1583   -2.0324    3.2269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5034    2.0768   -0.7421 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4707    1.4489   -1.5184 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8122    1.5157   -1.1422 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8276    0.8616   -1.9526 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1359    2.7713    0.4104 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2056    2.8381    0.7865 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1797    2.2104    0.0102 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2981   -1.8517   -0.6125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7082   -0.0878    0.9940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8496   -1.6165   -0.0408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3865    1.8332   -1.3712 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5436   -3.5436   -0.1732 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3134   -2.2912   -1.3957 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7551   -1.3879    1.9117 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0266   -2.9987    1.8437 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3889   -2.4656    0.0626 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1011   -0.8590    0.1530 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5854   -0.3074    2.1720 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7985   -1.5697    3.3924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1692    0.6238    0.3870 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8601   -3.4154   -0.6417 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7982   -2.0472   -0.0566 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4984   -1.3803    3.6389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0492   -0.5502    2.1865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8989   -2.1309   -3.0476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6665   -3.2790   -1.9100 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8350   -2.1342   -2.4942 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0923   -1.9982   -2.5936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5789   -3.4784    2.9703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1630   -2.7544    1.4776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1953   -1.5037   -2.7973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8307   -0.1479    0.1646 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0166    0.1024   -1.4402 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1712    0.1882   -2.9956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7567    1.9867    1.3963 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4972   -1.0972    2.7666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9310   -1.8183    4.2767 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0740    0.5449   -0.2918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4978   -3.7548   -2.3246 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1709    0.9069   -2.4122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9176    3.2504    0.9954 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0734   -2.6162    3.6022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4804   -3.1967    2.1982 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2261    2.2942    0.2896 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>
DB04073

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

> <ORIGINAL_SOURCE_URL>
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/UEIGEWJJVQHIAX-DLBZZEGUSA-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-DLBZZEGUSA-N

> <FORMULA>
C23H37N5O9

> <MOLECULAR_WEIGHT>
527.568

> <EXACT_MASS>
527.259127807

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
54.848903877653136

> <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-{[(2S,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_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
3

> <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-nitro-5-{[(2S,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-amino-propyl)-piperazin-1-yl]-propyl}-3-nitro-5-(galactopyranosyl)-beta-benzamide (DB04073)

Structure for N-{3-[4-(3-amino-propyl)-piperazin-1-yl]-propyl}-3-nitro-5-(galactopyranosyl)-beta-benzamide (DB04073)