3D structure for 1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione (DB08661)

25147495
  -OEChem-10051721253D

42 44  0     1  0  0  0  0  0999 V2000
    0.1871   -0.8949   -1.2521 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6225   -3.2114    0.0997 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3492   -2.3330    0.3258 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9668    1.9714    0.2605 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3188    0.4877    0.1393 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8482   -0.6047   -0.1331 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1427   -0.1814    0.2892 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5333   -0.9544   -0.7408 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4835   -1.8478    0.4916 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9771    0.4676   -0.4243 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0782   -1.6379    1.0039 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7078   -1.4608   -0.2849 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.3557    0.3393   -0.8816 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6240    1.7513    0.8096 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6180    0.7739   -0.1516 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1369    1.6989    0.9621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6748    0.7643   -0.2925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1221   -1.1313    0.1705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6535    1.6704   -0.1782 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0250    1.1922    0.1411 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4449    3.1403   -0.3541 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1554   -1.3860   -1.5326 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2446   -1.6451    1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2878    0.8941    0.3141 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8842    1.1083   -1.3113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3087   -2.4722    1.5975 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0368   -0.7330    1.6219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0283   -2.4368   -0.6688 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1822    0.9995   -1.7410 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4444   -0.6895   -1.2439 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1249    1.8365    1.7800 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3421    2.6147    0.1931 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3171    1.2799   -0.8251 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1348   -0.0904    0.2820 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4158    1.2815    1.9368 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5834    2.6953    0.8832 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5162   -3.3172   -0.2690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6807    1.1174   -0.5250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0690   -0.5377    0.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0630    3.5187   -1.1748 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4020    3.3816   -0.5851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7151    3.6771    0.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  1 12  1  0  0  0  0
  2  9  1  0  0  0  0
  2 37  1  0  0  0  0
  3 18  2  0  0  0  0
  4 20  2  0  0  0  0
  5 10  1  0  0  0  0
  5 13  1  0  0  0  0
  5 14  1  0  0  0  0
  6 12  1  0  0  0  0
  6 17  1  0  0  0  0
  6 18  1  0  0  0  0
  7 18  1  0  0  0  0
  7 20  1  0  0  0  0
  7 39  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  8 22  1  0  0  0  0
  9 11  1  0  0  0  0
  9 23  1  0  0  0  0
 10 24  1  0  0  0  0
 10 25  1  0  0  0  0
 11 12  1  0  0  0  0
 11 26  1  0  0  0  0
 11 27  1  0  0  0  0
 12 28  1  0  0  0  0
 13 15  1  0  0  0  0
 13 29  1  0  0  0  0
 13 30  1  0  0  0  0
 14 16  1  0  0  0  0
 14 31  1  0  0  0  0
 14 32  1  0  0  0  0
 15 16  1  0  0  0  0
 15 33  1  0  0  0  0
 15 34  1  0  0  0  0
 16 35  1  0  0  0  0
 16 36  1  0  0  0  0
 17 19  2  0  0  0  0
 17 38  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 40  1  0  0  0  0
 21 41  1  0  0  0  0
 21 42  1  0  0  0  0
M  END
> <DATABASE_ID>
DB08661

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

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

> <SMILES>
[H][C@@]1(O)C[C@]([H])(O[C@@]1([H])CN1CCCC1)N1C=C(C)C(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H21N3O4/c1-9-7-17(14(20)15-13(9)19)12-6-10(18)11(21-12)8-16-4-2-3-5-16/h7,10-12,18H,2-6,8H2,1H3,(H,15,19,20)/t10-,11+,12+/m1/s1

> <INCHI_KEY>
XUSBTLVYPZUOAW-WOPDTQHZSA-N

> <FORMULA>
C14H21N3O4

> <MOLECULAR_WEIGHT>
295.3342

> <EXACT_MASS>
295.153206175

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_NEUTRAL_MICROSPECIES_CHARGE>
0.9824043406971177

> <JCHEM_AVERAGE_POLARIZABILITY>
30.162803616012

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-[(2S,4R,5S)-4-hydroxy-5-[(pyrrolidin-1-yl)methyl]oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione

> <ALOGPS_LOGP>
-0.40

> <JCHEM_LOGP>
-0.26312599181953433

> <ALOGPS_LOGS>
-0.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NEUTRAL_CHARGE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.04163237691382

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.989620383898817

> <JCHEM_PKA_STRONGEST_BASIC>
8.775259601670722

> <JCHEM_POLAR_SURFACE_AREA>
82.11000000000001

> <JCHEM_REFRACTIVITY>
74.67979999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.99e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
biotin

> <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 1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione (DB08661)

Structure for 1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione (DB08661)