3D structure for (2S,3R,4S,5S)-3,4-Dihydroxy-2-[(methylsulfanyl)methyl]-5-(4-oxo-4,5-dihydro-1H-pyrrolo[3,2-d]pyrimidin-7-yl)pyrrolidinium (DB03881)

5288855
  -OEChem-12241909233D

37 39  0     1  0  0  0  0  0999 V2000
   -2.3150   -2.9895    0.7246 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8199    2.7952   -1.2085 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9386    1.8379    0.2299 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9546   -0.0261   -0.2119 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6166    0.0466    1.1416 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.6240    1.8938    0.2851 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9302   -1.1790   -0.0280 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2958   -1.6752   -0.3131 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0052    1.2927    0.5210 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8806   -0.3270    0.3894 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7630    1.4391   -0.8003 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1530    0.8892   -0.4903 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4895    1.2589    0.3798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6164   -1.6014   -0.3997 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2924    0.1173    0.1357 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3396    2.3410    0.4673 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6180    0.5378    0.0811 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6307   -0.3773   -0.1470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0502   -4.2815   -0.5122 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9837   -1.9925   -0.2445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2752    2.1119    1.2011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6641   -0.4686    1.1432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9553   -0.7417    1.1466 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8374    0.2306    2.1302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2827    0.8551   -1.5949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7017    0.6480   -1.4064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7580   -1.4888   -1.0700 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4932   -1.8387   -1.0117 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3867    2.8377   -1.9975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7959    1.4204    0.4205 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1470    3.3903    0.6429 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4490    2.4777    0.2996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9406   -4.4021   -1.1346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8493   -5.2292   -0.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1907   -4.0353   -1.1413 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7466   -3.0420   -0.3820 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4366   -0.8544   -0.3798 H   0  0  0  0  0  0  0  0  0  0  0  0
  1 14  1  0  0  0  0
  1 19  1  0  0  0  0
  2 11  1  0  0  0  0
  2 29  1  0  0  0  0
  3 12  1  0  0  0  0
  3 30  1  0  0  0  0
  4 18  1  0  0  0  0
  4 37  1  0  0  0  0
  5  9  1  0  0  0  0
  5 10  1  0  0  0  0
  5 23  1  0  0  0  0
  5 24  1  0  0  0  0
  6 16  1  0  0  0  0
  6 17  1  0  0  0  0
  6 32  1  0  0  0  0
  7 15  1  0  0  0  0
  7 20  2  0  0  0  0
  8 18  2  0  0  0  0
  8 20  1  0  0  0  0
  9 11  1  0  0  0  0
  9 13  1  0  0  0  0
  9 21  1  0  0  0  0
 10 12  1  0  0  0  0
 10 14  1  0  0  0  0
 10 22  1  0  0  0  0
 11 12  1  0  0  0  0
 11 25  1  0  0  0  0
 12 26  1  0  0  0  0
 13 15  1  0  0  0  0
 13 16  2  0  0  0  0
 14 27  1  0  0  0  0
 14 28  1  0  0  0  0
 15 17  2  0  0  0  0
 16 31  1  0  0  0  0
 17 18  1  0  0  0  0
 19 33  1  0  0  0  0
 19 34  1  0  0  0  0
 19 35  1  0  0  0  0
 20 36  1  0  0  0  0
M  CHG  1   5   1
M  END
> <DATABASE_ID>
DB03881

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

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

> <SMILES>
[H]N1C=C([C@H]2[C@H](O)[C@H](O)[C@@H](CSC)[N+]2([H])[H])C2=C1C(=O)N=CN2[H]

> <INCHI_IDENTIFIER>
InChI=1S/C12H16N4O3S/c1-20-3-6-10(17)11(18)8(16-6)5-2-13-9-7(5)14-4-15-12(9)19/h2,4,6,8,10-11,13,16-18H,3H2,1H3,(H,14,15,19)/p+1/t6-,8+,10-,11+/m1/s1

> <INCHI_KEY>
CEGIKIXYDFDYDN-RXDXJJGDSA-O

> <FORMULA>
C12H17N4O3S

> <MOLECULAR_WEIGHT>
297.353

> <EXACT_MASS>
297.10213612

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_NEUTRAL_MICROSPECIES_CHARGE>
0.9659542686233332

> <JCHEM_AVERAGE_POLARIZABILITY>
29.184636860763973

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S)-3,4-dihydroxy-2-[(methylsulfanyl)methyl]-5-{4-oxo-1H,4H,5H-pyrrolo[3,2-d]pyrimidin-7-yl}pyrrolidin-1-ium

> <JCHEM_LOGP>
-0.719704893333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NEUTRAL_CHARGE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.17401738649519

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.50283583067725

> <JCHEM_PKA_STRONGEST_BASIC>
8.452943777979

> <JCHEM_POLAR_SURFACE_AREA>
114.32000000000001

> <JCHEM_REFRACTIVITY>
88.1875

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,5R)-5-(5-fluoro-2,4-dioxo-3H-pyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxyphosphonic acid

> <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 (2S,3R,4S,5S)-3,4-Dihydroxy-2-[(methylsulfanyl)methyl]-5-(4-oxo-4,5-dihydro-1H-pyrrolo[3,2-d]pyrimidin-7-yl)pyrrolidinium (DB03881)

Structure for (2S,3R,4S,5S)-3,4-Dihydroxy-2-[(methylsulfanyl)methyl]-5-(4-oxo-4,5-dihydro-1H-pyrrolo[3,2-d]pyrimidin-7-yl)pyrrolidinium (DB03881)