NP-MRD: Showing NP-Card for dADP (NP0002665)

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Record Information

Version

2.0

Created at

2020-11-23 18:26:24 UTC

Updated at

2021-08-12 19:51:48 UTC

NP-MRD ID

NP0002665

Secondary Accession Numbers

None

Natural Product Identification

Common Name

dADP

Provided By

BMRB

Description

DADP, also known as 2'-dADP, belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2. DADP exists in all living organisms, ranging from bacteria to humans. In humans, dADP is involved in the metabolic disorder called the gout or kelley-seegmiller syndrome pathway. DADP is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. dADP is found in Apis cerana and Daphnia pulex. dADP was first documented in 1969 (PMID: 11947151). Based on a literature review a small amount of articles have been published on dADP (PMID: 1545776) (PMID: 23721485) (PMID: 5316336).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


     RDKit          2D

 41 43  0  0  0  0  0  0  0  0999 V2000
   -5.3549   -3.8846    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2536   -2.3881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4990   -1.5520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3977   -0.0555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0510    0.6051    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8056   -0.2309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9069   -1.7275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5149   -2.2863    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5532   -1.1351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3510    0.1352    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7921    1.5272    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5350    3.0050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0500    3.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3584    3.7332    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6105    1.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5366    0.6904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4628   -0.4896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9477   -0.2775    0.0000 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.7356    1.2074    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1598   -1.7624    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4326   -0.0654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3588   -1.2454    0.0000 P   0  0  0  0  0  5  0  0  0  0  0  0
    7.5387   -0.3193    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1788   -2.1715    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849   -2.4253    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4662    0.8260    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7016   -4.5452    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1095   -4.7207    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6432    0.7805    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0567   -1.2364    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2350    1.9375    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0315    3.1063    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5907    4.5040    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4162    4.6717    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6155    5.2110    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8808    2.6681    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7166    1.6165    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3567   -0.2357    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9798   -2.6885    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3909   -3.6564    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7698   -2.2133    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 18 17  1  6
 18 19  2  0
 18 20  1  0
 18 21  1  0
 22 21  1  1
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
  7  2  1  0
 26 11  1  0
 10  6  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  9 30  1  0
 11 31  1  6
 12 32  1  6
 12 33  1  0
 13 34  1  1
 14 35  1  0
 15 36  1  6
 16 37  1  1
 16 38  1  0
 20 39  1  0
 24 40  1  0
 25 41  1  0
M  END

NP0002665
     RDKit          3D

 41 43  0  0  0  0  0  0  0  0999 V2000
   -6.8499    0.8204   -0.5073 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4975    0.5686   -0.7620 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1339    0.1007   -1.9708 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8261   -0.1706   -2.2295 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8557    0.0046   -1.3325 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2100    0.4599   -0.1340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5077    0.7562    0.1948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4973    1.1779    1.4700 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2314    1.1583    1.9508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4273    0.7086    0.9718 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0514    0.3667    1.0462 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9997   -1.1914    1.1251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -1.4833   -0.0327 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6343   -2.6643    0.1112 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7789   -0.2292    0.1044 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0891   -0.0710   -0.4419 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8893   -1.1909    0.0949 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9873   -0.4866    1.1839 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.0284   -1.4497    2.3982 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3865    0.9864    1.7727 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5044   -0.3723    0.6127 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7849    0.7713   -0.5853 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.0709    2.0557   -0.3732 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3004    0.1104   -2.0865 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4870    0.9963   -0.6145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2625    0.6960   -0.0924 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2972    1.7300   -0.7550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4680    0.0641   -0.0614 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4907   -0.5610   -3.2050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9179    1.4536    2.9568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5343    0.7881    1.8825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4543   -1.4493    2.0378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9554   -1.6363    0.9496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6172   -1.5191   -0.9889 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0387   -3.3833   -0.2789 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9233   -0.1943    1.3035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0773   -0.3358   -1.5463 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6265    0.8312   -0.2156 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5269    1.7496    1.2019 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1511   -0.8912   -1.9725 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8172    0.9247   -1.5243 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 18 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
  7  2  1  0
 26 11  1  0
 10  6  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  9 30  1  0
 11 31  1  1
 12 32  1  0
 12 33  1  0
 13 34  1  6
 14 35  1  0
 15 36  1  1
 16 37  1  0
 16 38  1  0
 20 39  1  0
 24 40  1  0
 25 41  1  0
M  END


     RDKit          2D

 41 43  0  0  0  0  0  0  0  0999 V2000
   -5.3549   -3.8846    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2536   -2.3881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4990   -1.5520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3977   -0.0555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0510    0.6051    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8056   -0.2309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9069   -1.7275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5149   -2.2863    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5532   -1.1351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3510    0.1352    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7921    1.5272    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5350    3.0050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0500    3.2171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3584    3.7332    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6105    1.8704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5366    0.6904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4628   -0.4896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9477   -0.2775    0.0000 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.7356    1.2074    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1598   -1.7624    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4326   -0.0654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3588   -1.2454    0.0000 P   0  0  0  0  0  5  0  0  0  0  0  0
    7.5387   -0.3193    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1788   -2.1715    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849   -2.4253    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4662    0.8260    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7016   -4.5452    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1095   -4.7207    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6432    0.7805    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0567   -1.2364    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2350    1.9375    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0315    3.1063    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5907    4.5040    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4162    4.6717    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6155    5.2110    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8808    2.6681    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7166    1.6165    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3567   -0.2357    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9798   -2.6885    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3909   -3.6564    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7698   -2.2133    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 18 17  1  6
 18 19  2  0
 18 20  1  0
 18 21  1  0
 22 21  1  1
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
  7  2  1  0
 26 11  1  0
 10  6  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  9 30  1  0
 11 31  1  6
 12 32  1  6
 12 33  1  0
 13 34  1  1
 14 35  1  0
 15 36  1  6
 16 37  1  1
 16 38  1  0
 20 39  1  0
 24 40  1  0
 25 41  1  0
M  END
> <DATABASE_ID>
NP0002665

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC=NC2=C1N=CN2[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N5O9P2/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(23-7)2-22-26(20,21)24-25(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1

> <INCHI_KEY>
DAEAPNUQQAICNR-RRKCRQDMSA-N

> <FORMULA>
C10H15N5O9P2

> <MOLECULAR_WEIGHT>
411.2017

> <EXACT_MASS>
411.034500127

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
33.60408616221964

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <ALOGPS_LOGP>
-1.57

> <JCHEM_LOGP>
-3.8208162402226273

> <ALOGPS_LOGS>
-2.17

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1392558743057477

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7688842589671903

> <JCHEM_PKA_STRONGEST_BASIC>
4.014841097084696

> <JCHEM_POLAR_SURFACE_AREA>
212.36999999999998

> <JCHEM_REFRACTIVITY>
83.43069999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.80e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dADP

> <JCHEM_VEBER_RULE>
0

$$$$

NP0002665
     RDKit          3D

 41 43  0  0  0  0  0  0  0  0999 V2000
   -6.8499    0.8204   -0.5073 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4975    0.5686   -0.7620 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1339    0.1007   -1.9708 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8261   -0.1706   -2.2295 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8557    0.0046   -1.3325 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2100    0.4599   -0.1340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5077    0.7562    0.1948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4973    1.1779    1.4700 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2314    1.1583    1.9508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4273    0.7086    0.9718 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0514    0.3667    1.0462 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9997   -1.1914    1.1251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -1.4833   -0.0327 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6343   -2.6643    0.1112 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7789   -0.2292    0.1044 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0891   -0.0710   -0.4419 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8893   -1.1909    0.0949 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9873   -0.4866    1.1839 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.0284   -1.4497    2.3982 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3865    0.9864    1.7727 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5044   -0.3723    0.6127 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7849    0.7713   -0.5853 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.0709    2.0557   -0.3732 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3004    0.1104   -2.0865 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4870    0.9963   -0.6145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2625    0.6960   -0.0924 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2972    1.7300   -0.7550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4680    0.0641   -0.0614 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4907   -0.5610   -3.2050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9179    1.4536    2.9568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5343    0.7881    1.8825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4543   -1.4493    2.0378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9554   -1.6363    0.9496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6172   -1.5191   -0.9889 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0387   -3.3833   -0.2789 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9233   -0.1943    1.3035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0773   -0.3358   -1.5463 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6265    0.8312   -0.2156 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5269    1.7496    1.2019 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1511   -0.8912   -1.9725 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8172    0.9247   -1.5243 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 18 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
  7  2  1  0
 26 11  1  0
 10  6  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  9 30  1  0
 11 31  1  1
 12 32  1  0
 12 33  1  0
 13 34  1  6
 14 35  1  0
 15 36  1  1
 16 37  1  0
 16 38  1  0
 20 39  1  0
 24 40  1  0
 25 41  1  0
M  END

HEADER    PROTEIN                                 18-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-SEP-20         0                                  
HETATM    1  C   UNK     0    8668.5678666.516   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8667.6208663.043   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8669.8998665.744   0.000  0.00  0.00           O+0
HETATM    4  P   UNK     0    8671.2318666.516   0.000  0.00  0.00           P+0
HETATM    5  O   UNK     0    8672.5798665.771   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8670.4658667.851   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8672.0058667.851   0.000  0.00  0.00           O+0
HETATM    8  P   UNK     0    8673.9158666.539   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0    8673.1418667.873   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8675.2438665.771   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8674.6818667.873   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    8665.9808666.667   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0    8665.2108664.297   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8666.7508664.297   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8667.2268665.762   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8659.4598666.722   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0    8658.9838665.258   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0    8660.0148664.113   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0    8661.5208664.433   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0    8661.9968665.898   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8660.9658667.042   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0    8663.4038666.524   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0    8663.2428668.055   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0    8661.7368668.376   0.000  0.00  0.00           N+0
HETATM   25  N   UNK     0    8658.4298667.866   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0    8664.7368665.754   0.000  0.00  0.00           C+0
CONECT    1    3   15                                                       
CONECT    2   14                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5    6    7                                             
CONECT    5    4    8                                                       
CONECT    6    4                                                            
CONECT    7    4                                                            
CONECT    8    5    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
CONECT   12   15   26                                                       
CONECT   13   14   26                                                       
CONECT   14   13   15    2                                                  
CONECT   15   14   12    1                                                  
CONECT   16   21   17   25                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   21   19   22                                                  
CONECT   21   20   16   24                                                  
CONECT   22   23   20   26                                                  
CONECT   23   24   22                                                       
CONECT   24   23   21                                                       
CONECT   25   16                                                            
CONECT   26   22   13   12                                                  
MASTER        0    0    0    0    0    0    0    0   26    0   56    0
END

COMPND    NP0002665
HETATM    1  N1  UNL     1      -6.850   0.820  -0.507  1.00  0.00           N  
HETATM    2  C1  UNL     1      -5.497   0.569  -0.762  1.00  0.00           C  
HETATM    3  N2  UNL     1      -5.134   0.101  -1.971  1.00  0.00           N  
HETATM    4  C2  UNL     1      -3.826  -0.171  -2.229  1.00  0.00           C  
HETATM    5  N3  UNL     1      -2.856   0.005  -1.332  1.00  0.00           N  
HETATM    6  C3  UNL     1      -3.210   0.460  -0.134  1.00  0.00           C  
HETATM    7  C4  UNL     1      -4.508   0.756   0.195  1.00  0.00           C  
HETATM    8  N4  UNL     1      -4.497   1.178   1.470  1.00  0.00           N  
HETATM    9  C5  UNL     1      -3.231   1.158   1.951  1.00  0.00           C  
HETATM   10  N5  UNL     1      -2.427   0.709   0.972  1.00  0.00           N  
HETATM   11  C6  UNL     1      -1.051   0.367   1.046  1.00  0.00           C  
HETATM   12  C7  UNL     1      -1.000  -1.191   1.125  1.00  0.00           C  
HETATM   13  C8  UNL     1      -0.017  -1.483  -0.033  1.00  0.00           C  
HETATM   14  O1  UNL     1       0.634  -2.664   0.111  1.00  0.00           O  
HETATM   15  C9  UNL     1       0.779  -0.229   0.104  1.00  0.00           C  
HETATM   16  C10 UNL     1       2.089  -0.071  -0.442  1.00  0.00           C  
HETATM   17  O2  UNL     1       2.889  -1.191   0.095  1.00  0.00           O  
HETATM   18  P1  UNL     1       3.987  -0.487   1.184  1.00  0.00           P  
HETATM   19  O3  UNL     1       4.028  -1.450   2.398  1.00  0.00           O  
HETATM   20  O4  UNL     1       3.386   0.986   1.773  1.00  0.00           O  
HETATM   21  O5  UNL     1       5.504  -0.372   0.613  1.00  0.00           O  
HETATM   22  P2  UNL     1       5.785   0.771  -0.585  1.00  0.00           P  
HETATM   23  O6  UNL     1       5.071   2.056  -0.373  1.00  0.00           O  
HETATM   24  O7  UNL     1       5.300   0.110  -2.087  1.00  0.00           O  
HETATM   25  O8  UNL     1       7.487   0.996  -0.614  1.00  0.00           O  
HETATM   26  O9  UNL     1      -0.263   0.696  -0.092  1.00  0.00           O  
HETATM   27  H1  UNL     1      -7.297   1.730  -0.755  1.00  0.00           H  
HETATM   28  H2  UNL     1      -7.468   0.064  -0.061  1.00  0.00           H  
HETATM   29  H3  UNL     1      -3.491  -0.561  -3.205  1.00  0.00           H  
HETATM   30  H4  UNL     1      -2.918   1.454   2.957  1.00  0.00           H  
HETATM   31  H5  UNL     1      -0.534   0.788   1.883  1.00  0.00           H  
HETATM   32  H6  UNL     1      -0.454  -1.449   2.038  1.00  0.00           H  
HETATM   33  H7  UNL     1      -1.955  -1.636   0.950  1.00  0.00           H  
HETATM   34  H8  UNL     1      -0.617  -1.519  -0.989  1.00  0.00           H  
HETATM   35  H9  UNL     1       0.039  -3.383  -0.279  1.00  0.00           H  
HETATM   36  H10 UNL     1       0.923  -0.194   1.303  1.00  0.00           H  
HETATM   37  H11 UNL     1       2.077  -0.336  -1.546  1.00  0.00           H  
HETATM   38  H12 UNL     1       2.627   0.831  -0.216  1.00  0.00           H  
HETATM   39  H13 UNL     1       3.527   1.750   1.202  1.00  0.00           H  
HETATM   40  H14 UNL     1       5.151  -0.891  -1.972  1.00  0.00           H  
HETATM   41  H15 UNL     1       7.817   0.925  -1.524  1.00  0.00           H  
CONECT    1    2   27   28
CONECT    2    3    3    7
CONECT    3    4
CONECT    4    5    5   29
CONECT    5    6
CONECT    6    7    7   10
CONECT    7    8
CONECT    8    9    9
CONECT    9   10   30
CONECT   10   11
CONECT   11   12   26   31
CONECT   12   13   32   33
CONECT   13   14   15   34
CONECT   14   35
CONECT   15   16   26   36
CONECT   16   17   37   38
CONECT   17   18
CONECT   18   19   19   20   21
CONECT   20   39
CONECT   21   22
CONECT   22   23   23   24   25
CONECT   24   40
CONECT   25   41
END

NP0002665
     RDKit          3D

41 43  0  0  0  0  0  0  0  0999 V2000
   -6.8499    0.8204   -0.5073 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4975    0.5686   -0.7620 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1339    0.1007   -1.9708 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8261   -0.1706   -2.2295 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8557    0.0046   -1.3325 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2100    0.4599   -0.1340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5077    0.7562    0.1948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4973    1.1779    1.4700 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2314    1.1583    1.9508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4273    0.7086    0.9718 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0514    0.3667    1.0462 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9997   -1.1914    1.1251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -1.4833   -0.0327 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6343   -2.6643    0.1112 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7789   -0.2292    0.1044 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0891   -0.0710   -0.4419 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8893   -1.1909    0.0949 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9873   -0.4866    1.1839 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.0284   -1.4497    2.3982 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3865    0.9864    1.7727 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5044   -0.3723    0.6127 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7849    0.7713   -0.5853 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.0709    2.0557   -0.3732 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3004    0.1104   -2.0865 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4870    0.9963   -0.6145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2625    0.6960   -0.0924 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2972    1.7300   -0.7550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4680    0.0641   -0.0614 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4907   -0.5610   -3.2050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9179    1.4536    2.9568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5343    0.7881    1.8825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4543   -1.4493    2.0378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9554   -1.6363    0.9496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6172   -1.5191   -0.9889 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0387   -3.3833   -0.2789 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9233   -0.1943    1.3035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0773   -0.3358   -1.5463 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6265    0.8312   -0.2156 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5269    1.7496    1.2019 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1511   -0.8912   -1.9725 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8172    0.9247   -1.5243 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 18 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
  7  2  1  0
 26 11  1  0
 10  6  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  9 30  1  0
 11 31  1  1
 12 32  1  0
 12 33  1  0
 13 34  1  6
 14 35  1  0
 15 36  1  1
 16 37  1  0
 16 38  1  0
 20 39  1  0
 24 40  1  0
 25 41  1  0
M  END

View in JSmol

Synonyms

Value	Source
2'-Deoxyadenosine 5'-diphosphate	ChEBI
2'-DEOXYADENOSINE-5'-diphosphATE	ChEBI
Deoxyadenosine diphosphate	ChEBI
2'-Deoxyadenosine 5'-diphosphoric acid	Generator
2'-DEOXYADENOSINE-5'-diphosphoric acid	Generator
Deoxyadenosine diphosphoric acid	Generator
2'-Deoxyadenosine 5'-(trihydrogen diphosphate)	HMDB
2'-Deoxyadenosine 5'-pyrophosphate	HMDB
2'-Deoxyadenosine diphosphate	HMDB
2'-dADP	HMDB
2’-deoxyadenosine 5’-(trihydrogen diphosphate)	HMDB
2’-deoxyadenosine 5’-diphosphate	HMDB
2’-deoxyadenosine 5’-pyrophosphate	HMDB
2’-deoxyadenosine diphosphate	HMDB
2’-dADP	HMDB
Deoxyadenosine 5'-diphosphate	HMDB
Deoxyadenosine 5’-diphosphate	HMDB
2’-deoxyadenosine-5’-diphosphate	HMDB
2’-deoxyadenosine-5’-diphosphoric acid	HMDB
dADP	HMDB

Chemical Formula

C₁₀H₁₅N₅O₉P₂

Average Mass

411.2017 Da

Monoisotopic Mass

411.03450 Da

IUPAC Name

[({[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

dADP

CAS Registry Number

Not Available

SMILES

NC1=NC=NC2=C1N=CN2[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1

InChI Identifier

InChI=1S/C10H15N5O9P2/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(23-7)2-22-26(20,21)24-25(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1

InChI Key

DAEAPNUQQAICNR-RRKCRQDMSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Achyrocline flaccida	KNApSAcK Database	22123792
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Andromeda polifolia	KNApSAcK Database	22123792
Anser anser	FooDB	FooDB
Apis cerana	LOTUS Database	35616633
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Cheilanthes kaulfussii	KNApSAcK Database	22123792
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Daphnia pulex	LOTUS Database	35616633
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Eremophila alternifolia	KNApSAcK Database	22123792
Eremophila racemosissima	KNApSAcK Database	22123792
Gallus gallus	FooDB	FooDB
Helichrysum aureum	KNApSAcK Database	22123792
Helichrysum graveolen	KNApSAcK Database	22123792
Helichrysum picardii	KNApSAcK Database	22123792
Heliotropium filifolium	KNApSAcK Database	22123792
Heliotropium huascoense	KNApSAcK Database	22123792
Heliotropium huascuense	KNApSAcK Database	22123792
Heliotropium megalanthum	KNApSAcK Database	22123792
Heliotropium pycnophyllum	KNApSAcK Database	22123792
Heliotropium sinuatum	KNApSAcK Database	22123792
Heliotropium stenophyllum	KNApSAcK Database	22123792
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Lychnophora markgravii	KNApSAcK Database	22123792
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Nothofagus spp.	KNApSAcK Database	22123792
Notholaena candida	KNApSAcK Database	22123792
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Ozothamnus spp.	KNApSAcK Database	22123792
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Populus nigra	KNApSAcK Database	22123792
Pseudognaphalium cheiranthifolium	KNApSAcK Database	22123792
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB
Woodsia scopulina	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine deoxyribonucleotides

Direct Parent

Purine 2'-deoxyribonucleoside diphosphates

Alternative Parents

Not Available

Substituents

Not Available

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.6	ALOGPS
logP	-3.8	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	4.01	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	212.37 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	83.43 m³·mol⁻¹	ChemAxon
Polarizability	33.6 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

HMDB0001508

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Deoxyadenosine_diphosphate

METLIN ID

Not Available

PubChem Compound

188966

PDB ID

Not Available

ChEBI ID

16174

Good Scents ID

Not Available

References

General References

Kaufmann G, Littauer UZ: Deoxyadenosine diphosphate as substrate for polynucleotide phosphorylase from Escherichia coli. FEBS Lett. 1969 Jul;4(2):79-83. doi: 10.1016/0014-5793(69)80201-2. [PubMed:11947151 ]
Schwanstecher C, Dickel C, Panten U: Cytosolic nucleotides enhance the tolbutamide sensitivity of the ATP-dependent K+ channel in mouse pancreatic B cells by their combined actions at inhibitory and stimulatory receptors. Mol Pharmacol. 1992 Mar;41(3):480-6. [PubMed:1545776 ]
Das U, Wang LK, Smith P, Shuman S: Structural and biochemical analysis of the phosphate donor specificity of the polynucleotide kinase component of the bacterial pnkp*hen1 RNA repair system. Biochemistry. 2013 Jul 9;52(27):4734-43. doi: 10.1021/bi400412x. Epub 2013 Jun 26. [PubMed:23721485 ]
Chou JY, Singer MF: Deoxyadenosine diphosphate as a substrate and inhibitor of polynucleotide phosphorylase of Micrococcus luteus. I. Deoxyadenosine diphosphate as a substrate for polymerization and the exchange reaction with inorganic 32 P. J Biol Chem. 1971 Dec 25;246(24):7486-96. [PubMed:5316336 ]

Showing NP-Card for dADP (NP0002665)

MOL for NP0002665 (dADP)

3D MOL for NP0002665 (dADP)

3D SDF for NP0002665 (dADP)

3D-SDF for NP0002665 (dADP)

PDB for NP0002665 (dADP)

3D PDB for NP0002665 (dADP)

SMILES for NP0002665 (dADP)

INCHI for NP0002665 (dADP)

Structure for NP0002665 (dADP)

3D Structure for NP0002665 (dADP)