3D structure for 2'-deoxy-N-(naphthalen-1-ylmethyl)guanosine 5'-(dihydrogen phosphate) (DB08237)

46937134
  -OEChem-10051721173D

56 60  0     1  0  0  0  0  0999 V2000
    0.2597    2.9249    1.3309 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7085    1.1607   -1.2439 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1133    2.9592   -1.8725 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8045    2.6730    0.1369 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8528   -4.7403    1.2110 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1434    4.3951    1.8702 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2486    1.9434    2.5114 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6999    2.7660    0.9400 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6511   -0.9856   -0.5501 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2574   -0.9516   -0.1209 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0509   -3.0732    0.1706 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3905   -2.9864    0.8147 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9709   -1.1444    0.3645 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9153    0.3853   -1.1201 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.4817    2.6249   -0.6389 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8716    1.2129   -0.2684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9763    2.5208   -0.8465 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1858    2.8034    0.4239 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4728   -1.5050   -0.1348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5835   -1.9778   -0.3445 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7242   -2.7730    0.3014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2296   -1.7519    0.3743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6498   -3.5991    0.8147 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1801   -1.7830    0.8308 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3447   -0.8465    0.7377 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9713   -0.5563   -0.4852 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0689    0.3367   -0.5057 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7939   -0.2643    1.9234 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5325   -1.1331   -1.6882 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5077    0.9134    0.6973 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8733    0.6138    1.9033 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6955    0.6268   -1.7287 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1669   -0.8335   -2.8941 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2463    0.0447   -2.9143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3093    0.2050   -2.1275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7827    3.3662    0.1068 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6872    1.0393    0.7986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9167    0.9705   -0.4844 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6211    3.1644   -1.6591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4469    2.0862    1.2085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3928    3.8172    0.7800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8123    3.8501   -2.1202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6280   -1.8427   -0.5900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0684   -0.0083   -0.4434 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0384   -0.1893    0.0232 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3831   -2.7053    0.2728 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0396   -2.1022    1.8719 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3114   -0.4811    2.8730 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2897    1.8644    3.3275 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4212    4.8230    2.5487 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6944   -1.8227   -1.7317 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3493    1.6030    0.7052 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2218    1.0677    2.8264 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5410    1.3105   -1.7681 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8177   -1.2856   -3.8180 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7396    0.2776   -3.8536 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  1  6  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  2  0  0  0  0
  2 14  1  0  0  0  0
  2 17  1  0  0  0  0
  3 15  1  0  0  0  0
  3 42  1  0  0  0  0
  4 18  1  0  0  0  0
  5 23  2  0  0  0  0
  6 50  1  0  0  0  0
  7 49  1  0  0  0  0
  9 14  1  0  0  0  0
  9 19  1  0  0  0  0
  9 20  1  0  0  0  0
 10 19  1  0  0  0  0
 10 22  1  0  0  0  0
 10 44  1  0  0  0  0
 11 20  2  0  0  0  0
 11 21  1  0  0  0  0
 12 22  2  0  0  0  0
 12 23  1  0  0  0  0
 13 22  1  0  0  0  0
 13 24  1  0  0  0  0
 13 45  1  0  0  0  0
 14 16  1  0  0  0  0
 14 35  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 36  1  0  0  0  0
 16 37  1  0  0  0  0
 16 38  1  0  0  0  0
 17 18  1  0  0  0  0
 17 39  1  0  0  0  0
 18 40  1  0  0  0  0
 18 41  1  0  0  0  0
 19 21  2  0  0  0  0
 20 43  1  0  0  0  0
 21 23  1  0  0  0  0
 24 25  1  0  0  0  0
 24 46  1  0  0  0  0
 24 47  1  0  0  0  0
 25 26  1  0  0  0  0
 25 28  2  0  0  0  0
 26 27  1  0  0  0  0
 26 29  2  0  0  0  0
 27 30  1  0  0  0  0
 27 32  2  0  0  0  0
 28 31  1  0  0  0  0
 28 48  1  0  0  0  0
 29 33  1  0  0  0  0
 29 51  1  0  0  0  0
 30 31  2  0  0  0  0
 30 52  1  0  0  0  0
 31 53  1  0  0  0  0
 32 34  1  0  0  0  0
 32 54  1  0  0  0  0
 33 34  2  0  0  0  0
 33 55  1  0  0  0  0
 34 56  1  0  0  0  0
M  END
> <DATABASE_ID>
DB08237

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

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

> <SMILES>
[H][C@]1(O)C[C@@]([H])(O[C@]1([H])COP(O)(O)=O)N1C=NC2=C1N=C(NCC1=CC=CC3=C1C=CC=C3)NC2=O

> <INCHI_IDENTIFIER>
InChI=1S/C21H22N5O7P/c27-15-8-17(33-16(15)10-32-34(29,30)31)26-11-23-18-19(26)24-21(25-20(18)28)22-9-13-6-3-5-12-4-1-2-7-14(12)13/h1-7,11,15-17,27H,8-10H2,(H2,29,30,31)(H2,22,24,25,28)/t15-,16+,17+/m0/s1

> <INCHI_KEY>
COMPKRGNHXOXMN-GVDBMIGSSA-N

> <FORMULA>
C21H22N5O7P

> <MOLECULAR_WEIGHT>
487.4024

> <EXACT_MASS>
487.125684595

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_NEUTRAL_MICROSPECIES_CHARGE>
-1.9179765727145495

> <JCHEM_AVERAGE_POLARIZABILITY>
47.481889949447066

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,5R)-3-hydroxy-5-(2-{[(naphthalen-1-yl)methyl]amino}-6-oxo-6,9-dihydro-1H-purin-9-yl)oxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
0.31

> <JCHEM_LOGP>
0.7646450347518595

> <ALOGPS_LOGS>
-3.01

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NEUTRAL_CHARGE>
-2

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.257704512758724

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3024640447946767

> <JCHEM_PKA_STRONGEST_BASIC>
0.4081746634804658

> <JCHEM_POLAR_SURFACE_AREA>
167.53

> <JCHEM_REFRACTIVITY>
119.8207

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.78e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
tetrahydrofolic 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 2'-deoxy-N-(naphthalen-1-ylmethyl)guanosine 5'-(dihydrogen phosphate) (DB08237)

Structure for 2'-deoxy-N-(naphthalen-1-ylmethyl)guanosine 5'-(dihydrogen phosphate) (DB08237)