3D structure for 5-(6-D-ribitylamino-2,4-dihydroxypyrimidin-5-yl)-1-pentyl-phosphonic acid (DB04266)

445357
  -OEChem-01152014063D

53 53  0     1  0  0  0  0  0999 V2000
   -6.2312    0.1477    0.3955 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.6881   -2.2951   -1.8054 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5383   -2.6695    1.6582 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1626   -4.5109    0.4540 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7118   -6.4687   -0.2357 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3780   -0.4067   -0.5890 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7252   -1.1631    1.1812 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5645    4.5878   -0.5976 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5982    1.3185    1.2383 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5891    3.6112    1.3924 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1410    0.0974   -0.3711 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3293    1.9143    0.4983 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5776    4.1168    0.4012 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7881   -2.2572   -0.3813 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4544   -2.7246    0.2349 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1795    1.6382   -0.3129 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0241    1.9464   -1.2606 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4560    1.1998   -1.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1679   -0.8336    0.0435 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2490    2.3033   -0.5433 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0675   -4.1565   -0.1809 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5726    0.8760   -0.0440 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2103    1.4335   -0.1549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8650    0.4724   -0.7412 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1289   -5.1829    0.2127 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4145    3.7671   -0.2590 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5723    3.2385    0.8057 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6090   -2.9126   -0.0731 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6305   -2.0658   -0.0624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8783    0.8448    0.3835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3987    2.5236    0.2975 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1442    1.0831   -1.9164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3158    2.7490   -1.9497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2450    0.3169   -1.6540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7827    1.9979   -1.7161 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1164   -0.5692   -0.4406 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3086   -0.7987    1.1301 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8881   -4.1983   -1.2614 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7668    1.7480    0.5918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2538    0.0681    0.6250 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3481   -0.2565   -0.8930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6954   -0.4263   -1.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1831    1.2676   -1.4248 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1039   -4.9837   -0.2370 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2419   -5.2446    1.2993 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0393    1.2487    0.7826 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5483   -2.0224   -2.1677 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6866   -2.9766    2.0133 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7166    5.1019    0.6076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3808   -5.4182    0.1802 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6350   -6.4304   -1.2044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2554   -0.6398   -0.2174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2859   -1.5408    1.8918 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  1  7  1  0  0  0  0
  1  9  2  0  0  0  0
  1 24  1  0  0  0  0
  2 14  1  0  0  0  0
  2 47  1  0  0  0  0
  3 15  1  0  0  0  0
  3 48  1  0  0  0  0
  4 21  1  0  0  0  0
  4 50  1  0  0  0  0
  5 25  1  0  0  0  0
  5 51  1  0  0  0  0
  6 52  1  0  0  0  0
  7 53  1  0  0  0  0
  8 26  2  0  0  0  0
 10 27  2  0  0  0  0
 11 19  1  0  0  0  0
 11 23  1  0  0  0  0
 11 41  1  0  0  0  0
 12 23  1  0  0  0  0
 12 27  1  0  0  0  0
 12 46  1  0  0  0  0
 13 26  1  0  0  0  0
 13 27  1  0  0  0  0
 13 49  1  0  0  0  0
 14 15  1  0  0  0  0
 14 19  1  0  0  0  0
 14 28  1  0  0  0  0
 15 21  1  0  0  0  0
 15 29  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 16 30  1  0  0  0  0
 16 31  1  0  0  0  0
 17 20  1  0  0  0  0
 17 32  1  0  0  0  0
 17 33  1  0  0  0  0
 18 22  1  0  0  0  0
 18 34  1  0  0  0  0
 18 35  1  0  0  0  0
 19 36  1  0  0  0  0
 19 37  1  0  0  0  0
 20 23  2  0  0  0  0
 20 26  1  0  0  0  0
 21 25  1  0  0  0  0
 21 38  1  0  0  0  0
 22 24  1  0  0  0  0
 22 39  1  0  0  0  0
 22 40  1  0  0  0  0
 24 42  1  0  0  0  0
 24 43  1  0  0  0  0
 25 44  1  0  0  0  0
 25 45  1  0  0  0  0
M  END
> <DATABASE_ID>
DB04266

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

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

> <SMILES>
[H]N(C[C@H](O)[C@H](O)[C@H](O)CO)C1=C(CCCCCP(O)(O)=O)C(=O)N([H])C(=O)N1[H]

> <INCHI_IDENTIFIER>
InChI=1S/C14H26N3O9P/c18-7-10(20)11(21)9(19)6-15-12-8(13(22)17-14(23)16-12)4-2-1-3-5-27(24,25)26/h9-11,18-21H,1-7H2,(H2,24,25,26)(H3,15,16,17,22,23)/t9-,10+,11-/m0/s1

> <INCHI_KEY>
BMATWAHJJFXMFA-AXFHLTTASA-N

> <FORMULA>
C14H26N3O9P

> <MOLECULAR_WEIGHT>
411.3447

> <EXACT_MASS>
411.140665957

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_NEUTRAL_MICROSPECIES_CHARGE>
-1.1126988811396281

> <JCHEM_AVERAGE_POLARIZABILITY>
39.33598140743253

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[5-(2,4-dioxo-6-{[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]amino}-1,2,3,4-tetrahydropyrimidin-5-yl)pentyl]phosphonic acid

> <ALOGPS_LOGP>
-1.55

> <JCHEM_LOGP>
-3.409161444000001

> <ALOGPS_LOGS>
-2.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NEUTRAL_CHARGE>
-1

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.20645854386611

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8105619904592758

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9741785782507915

> <JCHEM_POLAR_SURFACE_AREA>
208.68

> <JCHEM_REFRACTIVITY>
101.59000000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.75e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-5-methyl-2-oxopyrimidin-1-yl)oxolan-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 5-(6-D-ribitylamino-2,4-dihydroxypyrimidin-5-yl)-1-pentyl-phosphonic acid (DB04266)

Structure for 5-(6-D-ribitylamino-2,4-dihydroxypyrimidin-5-yl)-1-pentyl-phosphonic acid (DB04266)