MiMeDB: Showing metabocard for 5'-O-phosphonoadenylyl-(3'->5')-adenosine (MMDBc0055590)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:59:43 UTC

Update Date

2022-08-12 20:09:25 UTC

Metabolite ID

MMDBc0055590

Metabolite Identification

Common Name

5'-O-phosphonoadenylyl-(3'->5')-adenosine

Description

PAPA belongs to the class of organic compounds known as (3'->5')-dinucleotides. These are dinucleotides where the two bases are connected via a (3'->5')-phosphodiester linkage. Based on a literature review a significant number of articles have been published on PAPA.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221592D          

 53 58  0  0  1  0            999 V2000
    0.2896   -4.0594    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.4940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0038   -7.4221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2785   -7.2645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2624   -4.6725    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0992   -1.0091    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4346   -7.9319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0829   -4.5863    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4185   -5.3400    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3687   -0.5966    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8838   -1.2640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0477   -8.4840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6061   -7.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8054   -5.8920    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8761   -9.2910    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8323   -8.2290    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3907   -6.8700    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6141   -8.0182    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8916   -6.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4954   -3.8718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2254   -5.5115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5877   -0.2517    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.2287   -0.4242    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4944    0.4825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1998   -3.2137    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.0264   -2.1097    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3220   -1.1584    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0347   -3.2748    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0909   -5.4795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -0.1841    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -2.0486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4082   -0.3379    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.5867   -2.6617    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5581   -3.9023    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2282   -1.8239    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9068   -4.6295    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6320   -6.1369    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7432   -1.3316    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6288   -0.4794    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1135   -6.3413    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6986    0.1999    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  1  1  0  0  0
  8  2  1  1  0  0  0
 11  7  1  0  0  0  0
 12 11  1  0  0  0  0
 14  8  1  0  0  0  0
 14 13  1  0  0  0  0
 15  9  2  0  0  0  0
 16 10  2  0  0  0  0
 17  9  1  0  0  0  0
 18 10  1  0  0  0  0
 19 12  1  0  0  0  0
 20 13  1  0  0  0  0
 21 15  1  0  0  0  0
 22 16  1  0  0  0  0
 23  3  2  0  0  0  0
 23 15  1  0  0  0  0
 24  4  2  0  0  0  0
 24 16  1  0  0  0  0
 25  3  1  0  0  0  0
 25 17  2  0  0  0  0
 26  4  1  0  0  0  0
 26 18  2  0  0  0  0
 27  5  2  0  0  0  0
 27  9  1  0  0  0  0
 28  6  2  0  0  0  0
 28 10  1  0  0  0  0
 29  5  1  0  0  0  0
 29 17  1  0  0  0  0
 19 29  1  1  0  0  0
 30  6  1  0  0  0  0
 30 18  1  0  0  0  0
 20 30  1  1  0  0  0
 11 31  1  6  0  0  0
 12 32  1  6  0  0  0
 13 33  1  6  0  0  0
 39  2  1  0  0  0  0
 40  1  1  0  0  0  0
 41  7  1  0  0  0  0
 41 19  1  0  0  0  0
 42  8  1  0  0  0  0
 42 20  1  0  0  0  0
 14 43  1  1  0  0  0
 44 34  1  0  0  0  0
 44 35  1  0  0  0  0
 44 36  2  0  0  0  0
 44 39  1  0  0  0  0
 45 37  1  0  0  0  0
 45 38  2  0  0  0  0
 45 40  1  0  0  0  0
 45 43  1  0  0  0  0
  7 46  1  6  0  0  0
  8 47  1  6  0  0  0
 11 48  1  1  0  0  0
 12 49  1  1  0  0  0
 13 50  1  1  0  0  0
 14 51  1  1  0  0  0
 19 52  1  6  0  0  0
 20 53  1  6  0  0  0
M  CHG  3  34  -1  35  -1  37  -1
M  END


  Mrv1652306172221592D          

 53 58  0  0  1  0            999 V2000
    0.2896   -4.0594    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.4940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0038   -7.4221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2785   -7.2645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2624   -4.6725    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0992   -1.0091    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4346   -7.9319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0829   -4.5863    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4185   -5.3400    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3687   -0.5966    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8838   -1.2640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0477   -8.4840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6061   -7.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8054   -5.8920    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8761   -9.2910    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8323   -8.2290    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3907   -6.8700    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6141   -8.0182    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8916   -6.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4954   -3.8718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2254   -5.5115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5877   -0.2517    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.2287   -0.4242    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4944    0.4825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1998   -3.2137    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.0264   -2.1097    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3220   -1.1584    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0347   -3.2748    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0909   -5.4795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -0.1841    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -2.0486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4082   -0.3379    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.5867   -2.6617    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5581   -3.9023    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2282   -1.8239    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9068   -4.6295    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6320   -6.1369    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7432   -1.3316    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6288   -0.4794    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1135   -6.3413    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6986    0.1999    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  1  1  0  0  0
  8  2  1  1  0  0  0
 11  7  1  0  0  0  0
 12 11  1  0  0  0  0
 14  8  1  0  0  0  0
 14 13  1  0  0  0  0
 15  9  2  0  0  0  0
 16 10  2  0  0  0  0
 17  9  1  0  0  0  0
 18 10  1  0  0  0  0
 19 12  1  0  0  0  0
 20 13  1  0  0  0  0
 21 15  1  0  0  0  0
 22 16  1  0  0  0  0
 23  3  2  0  0  0  0
 23 15  1  0  0  0  0
 24  4  2  0  0  0  0
 24 16  1  0  0  0  0
 25  3  1  0  0  0  0
 25 17  2  0  0  0  0
 26  4  1  0  0  0  0
 26 18  2  0  0  0  0
 27  5  2  0  0  0  0
 27  9  1  0  0  0  0
 28  6  2  0  0  0  0
 28 10  1  0  0  0  0
 29  5  1  0  0  0  0
 29 17  1  0  0  0  0
 19 29  1  1  0  0  0
 30  6  1  0  0  0  0
 30 18  1  0  0  0  0
 20 30  1  1  0  0  0
 11 31  1  6  0  0  0
 12 32  1  6  0  0  0
 13 33  1  6  0  0  0
 39  2  1  0  0  0  0
 40  1  1  0  0  0  0
 41  7  1  0  0  0  0
 41 19  1  0  0  0  0
 42  8  1  0  0  0  0
 42 20  1  0  0  0  0
 14 43  1  1  0  0  0
 44 34  1  0  0  0  0
 44 35  1  0  0  0  0
 44 36  2  0  0  0  0
 44 39  1  0  0  0  0
 45 37  1  0  0  0  0
 45 38  2  0  0  0  0
 45 40  1  0  0  0  0
 45 43  1  0  0  0  0
  7 46  1  6  0  0  0
  8 47  1  6  0  0  0
 11 48  1  1  0  0  0
 12 49  1  1  0  0  0
 13 50  1  1  0  0  0
 14 51  1  1  0  0  0
 19 52  1  6  0  0  0
 20 53  1  6  0  0  0
M  CHG  3  34  -1  35  -1  37  -1
M  END
> <DATABASE_ID>
MMDBc0055590

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP([O-])(=O)O[C@]2([H])[C@@]([H])(COP([O-])([O-])=O)O[C@@]([H])(N3C=NC4=C(N)N=CN=C34)[C@]2([H])O)O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C20H26N10O13P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-12(32)11(31)7(41-19)1-40-45(37,38)43-14-8(2-39-44(34,35)36)42-20(13(14)33)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-33H,1-2H2,(H,37,38)(H2,21,23,25)(H2,22,24,26)(H2,34,35,36)/p-3/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1

> <INCHI_KEY>
GTUJJVSZIHQLHA-XPWFQUROSA-K

> <FORMULA>
C20H23N10O13P2

> <MOLECULAR_WEIGHT>
673.41

> <EXACT_MASS>
673.093775576

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
57.98359562742128

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-[(phosphonooxy)methyl]oxolan-3-yl phosphate

> <JCHEM_LOGP>
-8.057103430922531

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
1.9204743421455635

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1252980055032928

> <JCHEM_PKA_STRONGEST_BASIC>
4.220461463862909

> <JCHEM_POLAR_SURFACE_AREA>
349.4

> <JCHEM_REFRACTIVITY>
140.9929

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-[(phosphonooxy)methyl]oxolan-3-yl phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       0.541  -7.578   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.061  -2.789   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.607 -13.855   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.520 -13.560   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.490  -8.722   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.185  -1.884   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.678 -14.806   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.021  -8.561   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.648  -9.968   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.555  -1.114   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.650  -2.359   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.822 -15.837   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -2.998 -13.300   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.503 -10.998   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -3.502 -17.343   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       4.924   5.923   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0      -5.287 -15.361   0.000  0.00  0.00           N+0
HETATM   24  N   UNK     0       6.258   3.613   0.000  0.00  0.00           N+0
HETATM   25  N   UNK     0      -4.463 -12.824   0.000  0.00  0.00           N+0
HETATM   26  N   UNK     0       4.924   1.303   0.000  0.00  0.00           N+0
HETATM   27  N   UNK     0      -1.146 -14.967   0.000  0.00  0.00           N+0
HETATM   28  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   29  N   UNK     0      -1.664 -12.530   0.000  0.00  0.00           N+0
HETATM   30  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM   31  O   UNK     0      -2.791  -7.227   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -4.154 -10.288   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       4.095  -1.114   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -1.097  -0.470   0.000  0.00  0.00           O-1
HETATM   35  O   UNK     0      -4.160  -0.792   0.000  0.00  0.00           O-1
HETATM   36  O   UNK     0      -2.790   0.901   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       2.240  -5.999   0.000  0.00  0.00           O-1
HETATM   38  O   UNK     0      -0.049  -3.938   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      -2.468  -2.162   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       0.065  -6.113   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      -0.170 -10.228   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       0.185  -0.344   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       2.126  -3.824   0.000  0.00  0.00           O+0
HETATM   44  P   UNK     0      -2.629  -0.631   0.000  0.00  0.00           P+0
HETATM   45  P   UNK     0       1.095  -4.969   0.000  0.00  0.00           P+0
HETATM   46  H   UNK     0      -1.042  -7.284   0.000  0.00  0.00           H+0
HETATM   47  H   UNK     0       0.426  -3.405   0.000  0.00  0.00           H+0
HETATM   48  H   UNK     0      -3.559  -8.642   0.000  0.00  0.00           H+0
HETATM   49  H   UNK     0      -3.046 -11.455   0.000  0.00  0.00           H+0
HETATM   50  H   UNK     0       3.254  -2.486   0.000  0.00  0.00           H+0
HETATM   51  H   UNK     0       1.174  -0.895   0.000  0.00  0.00           H+0
HETATM   52  H   UNK     0      -0.212 -11.837   0.000  0.00  0.00           H+0
HETATM   53  H   UNK     0       3.171   0.373   0.000  0.00  0.00           H+0
CONECT    1    7   40                                                       
CONECT    2    8   39                                                       
CONECT    3   23   25                                                       
CONECT    4   24   26                                                       
CONECT    5   27   29                                                       
CONECT    6   28   30                                                       
CONECT    7    1   11   41   46                                             
CONECT    8    2   14   42   47                                             
CONECT    9   15   17   27                                                  
CONECT   10   16   18   28                                                  
CONECT   11    7   12   31   48                                             
CONECT   12   11   19   32   49                                             
CONECT   13   14   20   33   50                                             
CONECT   14    8   13   43   51                                             
CONECT   15    9   21   23                                                  
CONECT   16   10   22   24                                                  
CONECT   17    9   25   29                                                  
CONECT   18   10   26   30                                                  
CONECT   19   12   29   41   52                                             
CONECT   20   13   30   42   53                                             
CONECT   21   15                                                            
CONECT   22   16                                                            
CONECT   23    3   15                                                       
CONECT   24    4   16                                                       
CONECT   25    3   17                                                       
CONECT   26    4   18                                                       
CONECT   27    5    9                                                       
CONECT   28    6   10                                                       
CONECT   29    5   17   19                                                  
CONECT   30    6   18   20                                                  
CONECT   31   11                                                            
CONECT   32   12                                                            
CONECT   33   13                                                            
CONECT   34   44                                                            
CONECT   35   44                                                            
CONECT   36   44                                                            
CONECT   37   45                                                            
CONECT   38   45                                                            
CONECT   39    2   44                                                       
CONECT   40    1   45                                                       
CONECT   41    7   19                                                       
CONECT   42    8   20                                                       
CONECT   43   14   45                                                       
CONECT   44   34   35   36   39                                             
CONECT   45   37   38   40   43                                             
CONECT   46    7                                                            
CONECT   47    8                                                            
CONECT   48   11                                                            
CONECT   49   12                                                            
CONECT   50   13                                                            
CONECT   51   14                                                            
CONECT   52   19                                                            
CONECT   53   20                                                            
MASTER        0    0    0    0    0    0    0    0   53    0  116    0
END

Synonyms

Value	Source
5'-O-Phosphonoadenylyl-(3'->5')-adenosine	ChEBI
5'-O-Phosphonoadenylyl-(3'->5')-adenosine(3-)	ChEBI

Molecular Formula

C₂₀H₂₃N₁₀O₁₃P₂

Average Mass

673.41

Monoisotopic Mass

673.093775576

IUPAC Name

[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-[(phosphonooxy)methyl]oxolan-3-yl phosphate

Traditional Name

[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-[(phosphonooxy)methyl]oxolan-3-yl phosphate

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP([O-])(=O)O[C@]2([H])[C@@]([H])(COP([O-])([O-])=O)O[C@@]([H])(N3C=NC4=C(N)N=CN=C34)[C@]2([H])O)O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C20H26N10O13P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-12(32)11(31)7(41-19)1-40-45(37,38)43-14-8(2-39-44(34,35)36)42-20(13(14)33)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-33H,1-2H2,(H,37,38)(H2,21,23,25)(H2,22,24,26)(H2,34,35,36)/p-3/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1

InChI Key

GTUJJVSZIHQLHA-XPWFQUROSA-K

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as (3'->5')-dinucleotides. These are dinucleotides where the two bases are connected via a (3'->5')-phosphodiester linkage.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

(3'->5')-dinucleotides and analogues

Sub Class

(3'->5')-dinucleotides

Direct Parent

(3'->5')-dinucleotides

Alternative Parents

Substituents

(3'->5')-dinucleotide
Purine ribonucleoside bisphosphate
Purine ribonucleoside 3',5'-bisphosphate
Purine ribonucleoside monophosphate
Ribonucleoside 3'-phosphate
Pentose-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
6-aminopurine
Purine
Imidazopyrimidine
Dialkyl phosphate
Aminopyrimidine
Imidolactam
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
N-substituted imidazole
Monosaccharide
Heteroaromatic compound
Tetrahydrofuran
Imidazole
Azole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-8.1	ChemAxon
pKa (Strongest Acidic)	1.13	ChemAxon
pKa (Strongest Basic)	4.22	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	349.4 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	140.99 m³·mol⁻¹	ChemAxon
Polarizability	57.98 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0016741	3',3'-c-di-AMP	5'-O-phosphonoadenylyl-(3'->5')-adenosine	Cyclic-di-AMP phosphodiesterase GdpP	Formation of 2'-nucleotide products from 2',3'-cyclic substrates	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	3	Human feces

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00000001

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Papa

METLIN ID

Not Available

PubChem Compound

129626759

PDB ID

Not Available

ChEBI ID

138171

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 5'-O-phosphonoadenylyl-(3'->5')-adenosine (MMDBc0055590)

MOL for #<Metabolite:0x000055c79b641c58>

3D MOL for #<Metabolite:0x000055c79b641c58>

3D SDF for #<Metabolite:0x000055c79b641c58>

3D-SDF for #<Metabolite:0x000055c79b641c58>

PDB for #<Metabolite:0x000055c79b641c58>

3D PDB for #<Metabolite:0x000055c79b641c58>

SMILES for #<Metabolite:0x000055c79b641c58>

INCHI for #<Metabolite:0x000055c79b641c58>

Structure for #<Metabolite:0x000055c79b641c58>

3D Structure for #<Metabolite:0x000055c79b641c58>