3D structure for GDP-alpha-D-mannuronic acid (DB04023)

447152
  -OEChem-11151918493D

63 66  0     1  0  0  0  0  0999 V2000
   -2.5073    2.8863    0.2302 P   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3884    1.3138   -2.0954 P   0  0  1  0  0  0  0  0  0  0  0  0
    1.6005    1.9708    1.2092 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4077    2.5771   -0.9524 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5370    4.3118    0.9498 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0286   -0.7610    0.1556 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0170    2.9314    0.8581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6787   -0.1268   -1.4253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3238   -4.2054   -0.1589 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9019   -3.2893   -1.1892 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4549   -2.6034    2.2214 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3092    2.0111   -1.1143 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7866   -0.8793    3.5745 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7345    4.3828   -0.3402 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5227    0.9790   -3.4204 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8779   -0.4672    2.3986 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5854    2.3870    1.1472 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6143    2.1422   -2.3496 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1559   -4.1717   -1.1254 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6280    0.1519    0.0839 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8724   -0.7666    0.2681 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6153   -1.6958   -0.6894 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0582   -3.0671   -0.3952 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9193   -1.8362    0.3644 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0446    2.5270   -0.5835 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5515    3.8159    0.0438 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7968    1.5302    0.5385 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3404    3.3458    0.8435 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0462    3.3933    0.0435 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0247   -2.8118   -0.1230 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0591   -2.4549   -1.2543 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4286   -2.4605    1.2399 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5954   -1.0036   -1.1360 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9198   -1.0203    1.2371 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5687   -0.8155   -0.0169 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4537   -0.4316   -0.3365 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9455   -1.9343   -0.4872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0650   -0.7549    2.4339 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6952   -3.1555   -0.7046 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5866   -1.9445    0.0568 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4461    2.2890   -1.4712 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3422    4.6026   -0.6868 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6096    1.5260    1.2749 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2188    3.9011    1.7804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1505    4.4216   -0.2727 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1125    2.7515   -0.8404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9749   -2.2804   -0.2591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5452   -2.6394   -2.2191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6319   -3.1680    1.4992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7875   -0.8307   -1.8546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7337   -0.2872    1.2276 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6566    1.6961   -1.2795 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1708    5.1097    1.3681 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5207    0.1128   -0.3749 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3406    0.0644    0.6145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6929   -4.4026   -1.0367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3349   -3.0657   -1.9468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1599   -1.9656    2.0169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2422   -0.7102    4.3728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1402    4.7336   -1.0367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3429    1.6976   -4.0634 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5488   -2.6236    0.2543 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3135   -0.9686    0.7114 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  1 12  1  0  0  0  0
  1 14  1  0  0  0  0
  1 17  2  0  0  0  0
  2  8  1  0  0  0  0
  2 12  1  0  0  0  0
  2 15  1  0  0  0  0
  2 18  2  0  0  0  0
  3 27  1  0  0  0  0
  3 28  1  0  0  0  0
  4 25  1  0  0  0  0
  4 52  1  0  0  0  0
  5 26  1  0  0  0  0
  5 53  1  0  0  0  0
  6 33  1  0  0  0  0
  6 34  1  0  0  0  0
  7 29  1  0  0  0  0
  8 33  1  0  0  0  0
  9 30  1  0  0  0  0
  9 56  1  0  0  0  0
 10 31  1  0  0  0  0
 10 57  1  0  0  0  0
 11 32  1  0  0  0  0
 11 58  1  0  0  0  0
 13 38  1  0  0  0  0
 13 59  1  0  0  0  0
 14 60  1  0  0  0  0
 15 61  1  0  0  0  0
 16 38  2  0  0  0  0
 19 39  2  0  0  0  0
 20 27  1  0  0  0  0
 20 35  1  0  0  0  0
 20 36  1  0  0  0  0
 21 35  1  0  0  0  0
 21 40  1  0  0  0  0
 21 55  1  0  0  0  0
 22 36  2  0  0  0  0
 22 37  1  0  0  0  0
 23 39  1  0  0  0  0
 23 40  2  0  0  0  0
 24 40  1  0  0  0  0
 24 62  1  0  0  0  0
 24 63  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 25 41  1  0  0  0  0
 26 28  1  0  0  0  0
 26 42  1  0  0  0  0
 27 43  1  0  0  0  0
 28 29  1  0  0  0  0
 28 44  1  0  0  0  0
 29 45  1  0  0  0  0
 29 46  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 30 47  1  0  0  0  0
 31 33  1  0  0  0  0
 31 48  1  0  0  0  0
 32 34  1  0  0  0  0
 32 49  1  0  0  0  0
 33 50  1  0  0  0  0
 34 38  1  0  0  0  0
 34 51  1  0  0  0  0
 35 37  2  0  0  0  0
 36 54  1  0  0  0  0
 37 39  1  0  0  0  0
M  END
> <DATABASE_ID>
DB04023

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

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

> <SMILES>
NC1=NC2=C(N=CN2[C@@H]2O[C@H](COP(O)(=O)OP(O)(=O)O[C@H]3O[C@@H]([C@@H](O)[C@H](O)[C@@H]3O)C(O)=O)[C@@H](O)[C@H]2O)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C16H23N5O17P2/c17-16-19-11-4(12(27)20-16)18-2-21(11)13-8(25)5(22)3(35-13)1-34-39(30,31)38-40(32,33)37-15-9(26)6(23)7(24)10(36-15)14(28)29/h2-3,5-10,13,15,22-26H,1H2,(H,28,29)(H,30,31)(H,32,33)(H3,17,19,20,27)/t3-,5-,6+,7+,8-,9+,10+,13-,15-/m1/s1

> <INCHI_KEY>
DNBSDUDYNPJVCN-ZXTXFPBHSA-N

> <FORMULA>
C16H23N5O17P2

> <MOLECULAR_WEIGHT>
619.3246

> <EXACT_MASS>
619.056417359

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
49.01305815291031

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4S,5S,6R)-6-({[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-3,4,5-trihydroxyoxane-2-carboxylic acid

> <ALOGPS_LOGP>
-1.56

> <JCHEM_LOGP>
-4.967309594999999

> <ALOGPS_LOGS>
-1.91

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.9123368793425857

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7164005662109842

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7320127240313705

> <JCHEM_POLAR_SURFACE_AREA>
344.4999999999999

> <JCHEM_REFRACTIVITY>
118.37869999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.60e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R)-2-(4-aminobutanamido)-3-{[(4-methoxyphenyl)methyl]sulfanyl}propanamido]acetic 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 GDP-alpha-D-mannuronic acid (DB04023)

Structure for GDP-alpha-D-mannuronic acid (DB04023)