3D structure for (2R,3S,5S)-2-(Hydroxymethyl)-5-[(2-sulfoethyl)carbamoyl]-3-pyrrolidiniumyl 2-acetamido-2-deoxy-4-O-sulfo-beta-D-glucopyranoside (DB02595)

5287797
  -OEChem-11211922223D

65 66  0     1  0  0  0  0  0999 V2000
   -5.9985    1.4152    0.5786 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.3831    2.9589    0.1592 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.5606   -0.4952 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3998    0.6930   -1.3692 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9783    0.8533   -0.5659 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5681   -4.8490   -2.1857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7899   -0.1634    1.8549 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6766   -0.7575    1.4828 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2492    1.9251   -3.6702 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3607   -1.0281    3.1902 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4099    1.5931   -0.2199 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1798    0.3581    1.5561 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5561    2.7309    1.0014 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0180    4.4897    0.5878 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5771    2.5909   -0.9904 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8267    2.8079    0.1542 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4343   -2.7039   -0.4709 N   0  3  0  0  0  0  0  0  0  0  0  0
   -1.4640   -1.8529    1.3141 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7096   -0.0787    0.5745 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0202   -1.1684   -1.5998 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1878   -2.6549   -1.3204 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2527   -1.4635   -0.7179 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4435   -0.6392   -1.7138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0547   -0.5173   -0.6974 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7381   -0.5835    0.6729 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4164   -3.4937   -2.5702 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2495   -0.3692    0.5481 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5748    0.8493   -0.3188 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7992    0.7965   -1.6376 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4967   -0.7459    0.5685 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0059    2.0512   -2.4800 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1723    0.7102    1.6933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7968   -1.9610    2.5209 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7334    2.1585    1.5928 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6687   -3.3909    2.9732 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4768   -0.9645   -2.5308 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3905   -3.0824   -0.7037 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1967   -1.8005   -1.1605 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8282   -0.8140   -2.7256 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4985    0.4354   -1.5098 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1625   -2.7606    0.5208 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9849   -3.5536   -0.6584 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3786   -1.3750   -1.3051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3229    0.2120    1.3060 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3115   -3.1859   -3.1205 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5527   -3.4209   -3.2390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7398   -1.2627    0.1422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2955    1.7640    0.2208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1077   -0.0699   -2.2383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7842   -2.6978    0.8492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0592    2.1860   -2.7436 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6489    2.9404   -1.9497 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3055   -0.1210   -0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3724    0.6293    2.2331 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7009   -5.3647   -2.9993 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7856    0.2718    2.6196 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2639    0.6295    1.7127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3931    2.7348   -4.1889 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6429    2.2462    1.5534 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1004    2.7061    2.4670 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2294   -3.9985    2.1767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0204   -3.4431    3.8523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6559   -3.7840    3.2309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1606    1.9331    0.3215 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5668    4.8697    1.3135 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  1 11  1  0  0  0  0
  1 12  2  0  0  0  0
  1 13  2  0  0  0  0
  2 14  1  0  0  0  0
  2 15  2  0  0  0  0
  2 16  2  0  0  0  0
  2 34  1  0  0  0  0
  3 20  1  0  0  0  0
  3 24  1  0  0  0  0
  4 24  1  0  0  0  0
  4 29  1  0  0  0  0
  5 28  1  0  0  0  0
  6 26  1  0  0  0  0
  6 55  1  0  0  0  0
  7 27  1  0  0  0  0
  7 54  1  0  0  0  0
  8 30  2  0  0  0  0
  9 31  1  0  0  0  0
  9 58  1  0  0  0  0
 10 33  2  0  0  0  0
 11 64  1  0  0  0  0
 14 65  1  0  0  0  0
 17 21  1  0  0  0  0
 17 22  1  0  0  0  0
 17 41  1  0  0  0  0
 17 42  1  0  0  0  0
 18 25  1  0  0  0  0
 18 33  1  0  0  0  0
 18 50  1  0  0  0  0
 19 30  1  0  0  0  0
 19 32  1  0  0  0  0
 19 53  1  0  0  0  0
 20 21  1  0  0  0  0
 20 23  1  0  0  0  0
 20 36  1  0  0  0  0
 21 26  1  0  0  0  0
 21 37  1  0  0  0  0
 22 23  1  0  0  0  0
 22 30  1  0  0  0  0
 22 38  1  0  0  0  0
 23 39  1  0  0  0  0
 23 40  1  0  0  0  0
 24 25  1  0  0  0  0
 24 43  1  0  0  0  0
 25 27  1  0  0  0  0
 25 44  1  0  0  0  0
 26 45  1  0  0  0  0
 26 46  1  0  0  0  0
 27 28  1  0  0  0  0
 27 47  1  0  0  0  0
 28 29  1  0  0  0  0
 28 48  1  0  0  0  0
 29 31  1  0  0  0  0
 29 49  1  0  0  0  0
 31 51  1  0  0  0  0
 31 52  1  0  0  0  0
 32 34  1  0  0  0  0
 32 56  1  0  0  0  0
 32 57  1  0  0  0  0
 33 35  1  0  0  0  0
 34 59  1  0  0  0  0
 34 60  1  0  0  0  0
 35 61  1  0  0  0  0
 35 62  1  0  0  0  0
 35 63  1  0  0  0  0
M  CHG  1  17   1
M  END
> <DATABASE_ID>
DB02595

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

> <ORIGINAL_SOURCE_URL>
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/RPNZWZDLNYCCIG-HMMVDTEZSA-O/SDF?record_type=3d

> <SMILES>
[H]N(CCS(O)(=O)=O)C(=O)[C@@H]1C[C@H](O[C@@H]2O[C@H](CO)[C@@H](OS(O)(=O)=O)[C@H](O)[C@H]2N([H])C(C)=O)[C@@H](CO)[N+]1([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C16H29N3O14S2/c1-7(22)18-12-13(23)14(33-35(28,29)30)11(6-21)32-16(12)31-10-4-8(19-9(10)5-20)15(24)17-2-3-34(25,26)27/h8-14,16,19-21,23H,2-6H2,1H3,(H,17,24)(H,18,22)(H,25,26,27)(H,28,29,30)/p+1/t8-,9+,10-,11+,12+,13+,14+,16+/m0/s1

> <INCHI_KEY>
RPNZWZDLNYCCIG-HMMVDTEZSA-O

> <FORMULA>
C16H30N3O14S2

> <MOLECULAR_WEIGHT>
552.551

> <EXACT_MASS>
552.116919063

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
50.87525863225148

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,5S)-3-{[(2R,3R,4R,5S,6R)-3-acetamido-4-hydroxy-6-(hydroxymethyl)-5-(sulfooxy)oxan-2-yl]oxy}-2-(hydroxymethyl)-5-[(2-sulfoethyl)carbamoyl]pyrrolidin-1-ium

> <ALOGPS_LOGP>
-1.26

> <JCHEM_LOGP>
-7.695688527380655

> <ALOGPS_LOGS>
-2.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
-1.0129468811275517

> <JCHEM_PKA_STRONGEST_ACIDIC>
-1.8683051529829782

> <JCHEM_PKA_STRONGEST_BASIC>
8.564890540341706

> <JCHEM_POLAR_SURFACE_AREA>
271.9299999999999

> <JCHEM_REFRACTIVITY>
121.67119999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.61e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
udp-6-sulfoquinovose

> <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 (2R,3S,5S)-2-(Hydroxymethyl)-5-[(2-sulfoethyl)carbamoyl]-3-pyrrolidiniumyl 2-acetamido-2-deoxy-4-O-sulfo-beta-D-glucopyranoside (DB02595)

Structure for (2R,3S,5S)-2-(Hydroxymethyl)-5-[(2-sulfoethyl)carbamoyl]-3-pyrrolidiniumyl 2-acetamido-2-deoxy-4-O-sulfo-beta-D-glucopyranoside (DB02595)