3D structure for N-naphthalen-1-ylmethyl-2'-[3,5-dimethoxybenzamido]-2'-deoxy-adenosine (DB03331)

446186
  -OEChem-12201914003D

72 77  0     1  0  0  0  0  0999 V2000
   -1.8829    4.1107   -0.6201 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7806    3.2837   -1.0952 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8742    6.4734    0.8948 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4238   -0.0906    1.7110 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3460   -4.9367    0.4799 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1876   -2.4567   -0.8899 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6818    2.1179   -0.1657 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7065    1.0602    0.1597 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2892    1.9556    0.8633 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6652    0.0427   -1.4280 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1077   -0.4438    0.4381 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3839   -1.2212   -1.0286 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1213    2.3512    0.3854 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0653    3.5115    0.1199 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9721    2.6734   -0.5639 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1045    4.6769   -0.0966 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7768    5.4202    1.1909 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1364    0.9355   -0.5779 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2116    2.6941    0.6980 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3019   -0.0692    0.8525 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0850    0.8534    0.0717 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8560   -0.2772   -0.1791 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9876   -1.3346    0.4840 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1706   -1.0058   -1.5919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2818   -1.3011   -0.0352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3370   -2.5562    0.6572 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9426   -1.5870    0.2163 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9805   -3.7443    0.3108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9252   -2.4892   -0.3815 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3589   -1.2931    0.6266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2746   -3.7107   -0.2086 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2987   -0.7601   -0.2708 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7135   -1.5716    1.9469 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6167   -0.5058    0.1777 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9594   -0.4738   -1.6033 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0094   -1.3212    2.3880 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9560   -0.7917    1.5102 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5565    0.0273   -0.7193 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9061    0.0554   -2.4808 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2023    0.3054   -2.0399 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0244   -4.8984    1.0160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7859   -3.7085   -1.2224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7728    2.4065    1.4251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7970    3.6691    0.9180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1717    2.3248   -1.5850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4700    5.3839   -0.8499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6806    5.8479    1.6355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2913    4.7644    1.9203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3635    0.9839   -0.6096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3424    4.0621   -1.2511 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0282    3.6443    1.1809 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6842    6.9313    1.7312 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1767   -1.7825   -2.2649 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3995    0.2750    1.0918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8300   -0.3709   -0.1556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3289   -2.5309    1.0571 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5584   -2.4270    0.8108 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8985   -1.9490   -0.8165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7209   -4.6676   -0.4588 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9886   -1.9815    2.6456 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9619   -0.6302   -2.0018 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2848   -1.5372    3.4162 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9631   -0.6039    1.8768 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5753    0.2311   -0.3963 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6304    0.2763   -3.5079 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9385    0.7184   -2.7233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6735   -5.9334    1.0837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0135   -4.4911    2.0328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3341   -4.3709    0.3489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2356   -4.2184   -2.0206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9153   -4.3407   -0.3373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7870   -3.4949   -1.6111 H   0  0  0  0  0  0  0  0  0  0  0  0
  1 15  1  0  0  0  0
  1 16  1  0  0  0  0
  2 14  1  0  0  0  0
  2 50  1  0  0  0  0
  3 17  1  0  0  0  0
  3 52  1  0  0  0  0
  4 20  2  0  0  0  0
  5 28  1  0  0  0  0
  5 41  1  0  0  0  0
  6 29  1  0  0  0  0
  6 42  1  0  0  0  0
  7 15  1  0  0  0  0
  7 18  1  0  0  0  0
  7 19  1  0  0  0  0
  8 13  1  0  0  0  0
  8 20  1  0  0  0  0
  8 49  1  0  0  0  0
  9 19  2  0  0  0  0
  9 21  1  0  0  0  0
 10 18  2  0  0  0  0
 10 24  1  0  0  0  0
 11 22  1  0  0  0  0
 11 27  1  0  0  0  0
 11 54  1  0  0  0  0
 12 22  1  0  0  0  0
 12 24  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 13 43  1  0  0  0  0
 14 16  1  0  0  0  0
 14 44  1  0  0  0  0
 15 45  1  0  0  0  0
 16 17  1  0  0  0  0
 16 46  1  0  0  0  0
 17 47  1  0  0  0  0
 17 48  1  0  0  0  0
 18 21  1  0  0  0  0
 19 51  1  0  0  0  0
 20 23  1  0  0  0  0
 21 22  2  0  0  0  0
 23 25  2  0  0  0  0
 23 26  1  0  0  0  0
 24 53  1  0  0  0  0
 25 29  1  0  0  0  0
 25 55  1  0  0  0  0
 26 28  2  0  0  0  0
 26 56  1  0  0  0  0
 27 30  1  0  0  0  0
 27 57  1  0  0  0  0
 27 58  1  0  0  0  0
 28 31  1  0  0  0  0
 29 31  2  0  0  0  0
 30 32  1  0  0  0  0
 30 33  2  0  0  0  0
 31 59  1  0  0  0  0
 32 34  1  0  0  0  0
 32 35  2  0  0  0  0
 33 36  1  0  0  0  0
 33 60  1  0  0  0  0
 34 37  1  0  0  0  0
 34 38  2  0  0  0  0
 35 39  1  0  0  0  0
 35 61  1  0  0  0  0
 36 37  2  0  0  0  0
 36 62  1  0  0  0  0
 37 63  1  0  0  0  0
 38 40  1  0  0  0  0
 38 64  1  0  0  0  0
 39 40  2  0  0  0  0
 39 65  1  0  0  0  0
 40 66  1  0  0  0  0
 41 67  1  0  0  0  0
 41 68  1  0  0  0  0
 41 69  1  0  0  0  0
 42 70  1  0  0  0  0
 42 71  1  0  0  0  0
 42 72  1  0  0  0  0
M  END
> <DATABASE_ID>
DB03331

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

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

> <SMILES>
[H]N(CC1=CC=CC2=CC=CC=C12)C1=C2N=CN([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3N([H])C(=O)C3=CC(OC)=CC(OC)=C3)C2=NC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C30H30N6O6/c1-40-20-10-19(11-21(12-20)41-2)29(39)35-24-26(38)23(14-37)42-30(24)36-16-34-25-27(32-15-33-28(25)36)31-13-18-8-5-7-17-6-3-4-9-22(17)18/h3-12,15-16,23-24,26,30,37-38H,13-14H2,1-2H3,(H,35,39)(H,31,32,33)/t23-,24-,26-,30-/m1/s1

> <INCHI_KEY>
OARVXDFNTLYMCJ-JVUUKAHWSA-N

> <FORMULA>
C30H30N6O6

> <MOLECULAR_WEIGHT>
570.5958

> <EXACT_MASS>
570.222682722

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_NEUTRAL_MICROSPECIES_CHARGE>
0.0049951649123715445

> <JCHEM_AVERAGE_POLARIZABILITY>
60.07214346683122

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(2R,3R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-2-(6-{[(naphthalen-1-yl)methyl]amino}-9H-purin-9-yl)oxolan-3-yl]-3,5-dimethoxybenzamide

> <ALOGPS_LOGP>
2.62

> <JCHEM_LOGP>
2.1754867969999996

> <ALOGPS_LOGS>
-4.50

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NEUTRAL_CHARGE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.186324320976357

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.298191424967282

> <JCHEM_PKA_STRONGEST_BASIC>
3.723806393492955

> <JCHEM_POLAR_SURFACE_AREA>
152.88

> <JCHEM_REFRACTIVITY>
154.44999999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.82e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-{3-[4-(3-aminopropyl)piperazin-1-yl]propyl}-3-[2-(thiophen-2-yl)acetamido]-5-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}benzamide

> <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 N-naphthalen-1-ylmethyl-2'-[3,5-dimethoxybenzamido]-2'-deoxy-adenosine (DB03331)

Structure for N-naphthalen-1-ylmethyl-2'-[3,5-dimethoxybenzamido]-2'-deoxy-adenosine (DB03331)