NP-MRD: Showing NP-Card for pppGpp (NP0339939)

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Record Information

Version

2.0

Created at

2024-09-12 00:20:51 UTC

Updated at

2024-09-12 00:20:52 UTC

NP-MRD ID

NP0339939

Secondary Accession Numbers

None

Natural Product Identification

Common Name

pppGpp

Description

Based on a literature review very few articles have been published on pppGpp.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05272302532D          

 40 42  0  0  0  0            999 V2000
   -0.5683   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -4.5353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1495   -5.0203    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6646   -5.6877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6344   -4.3528    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.8169   -5.5052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7307   -6.3257    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9102   -6.2394    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5512   -6.4119    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.6444   -7.1462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3119   -7.6311    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9793   -8.1160    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8270   -8.2985    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.7968   -6.9636    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0992   -3.2299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -2.4049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687   -2.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -3.4849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -4.2695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5867   -4.8826    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0347   -5.4957    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0264   -4.3306    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1998   -5.4346    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0283   -6.2416    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.2213   -6.0701    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8352   -6.4131    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8567   -7.0486    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 N   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
    4.0668   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 N   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
  1 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 22 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 26 29  1  0  0  0  0
 15 20  1  0  0  0  0
 17 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 37 39  2  0  0  0  0
 39 40  1  0  0  0  0
 33 40  2  0  0  0  0
 30 40  1  0  0  0  0
M  CHG  6   5  -1   9  -1  13  -1  14  -1  24  -1  29  -1
M  END


  Mrv2104 05272302532D          

 40 42  0  0  0  0            999 V2000
   -0.5683   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -4.5353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1495   -5.0203    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6646   -5.6877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6344   -4.3528    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.8169   -5.5052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7307   -6.3257    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9102   -6.2394    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5512   -6.4119    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.6444   -7.1462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3119   -7.6311    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9793   -8.1160    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8270   -8.2985    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.7968   -6.9636    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0992   -3.2299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -2.4049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687   -2.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -3.4849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -4.2695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5867   -4.8826    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0347   -5.4957    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0264   -4.3306    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1998   -5.4346    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0283   -6.2416    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.2213   -6.0701    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8352   -6.4131    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8567   -7.0486    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 N   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
    4.0668   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 N   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
  1 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 22 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 26 29  1  0  0  0  0
 15 20  1  0  0  0  0
 17 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 37 39  2  0  0  0  0
 39 40  1  0  0  0  0
 33 40  2  0  0  0  0
 30 40  1  0  0  0  0
M  CHG  6   5  -1   9  -1  13  -1  14  -1  24  -1  29  -1
M  END
> <DATABASE_ID>
NP0339939

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC2=C(N=CN2C2OC(COP([O-])(=O)OP([O-])(=O)OP([O-])([O-])=O)C(OP([O-])(=O)OP(O)([O-])=O)C2O)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1/C10H18N5O20P5/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(32-39(26,27)33-36(18,19)20)3(31-9)1-30-38(24,25)35-40(28,29)34-37(21,22)23/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H,28,29)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/p-6

> <INCHI_KEY>
KCPMACXZAITQAX-UHFFFAOYNA-H

> <FORMULA>
C10H12N5O20P5

> <MOLECULAR_WEIGHT>
677.093

> <EXACT_MASS>
676.879664276

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
46.555556897341575

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-6

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
hydrogen {[5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-4-hydroxy-2-({[oxido({[oxido(phosphonatooxy)phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-3-yl phosphonato]oxy}phosphonate

> <JCHEM_LOGP>
-4.218745695666666

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-6

> <JCHEM_PKA>
1.7409898550585374

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.838903958827889

> <JCHEM_POLAR_SURFACE_AREA>
404.84999999999997

> <JCHEM_REFRACTIVITY>
112.2554

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
hydrogen [5-(2-amino-6-oxo-1H-purin-9-yl)-4-hydroxy-2-({[oxido([oxido(phosphonatooxy)phosphoryl]oxy)phosphoryl]oxy}methyl)oxolan-3-yl phosphonato]oxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-23         0                                  
HETATM    1  C   UNK     0      -1.061  -6.934   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -0.900  -8.466   0.000  0.00  0.00           O+0
HETATM    3  P   UNK     0      -2.146  -9.371   0.000  0.00  0.00           P+0
HETATM    4  O   UNK     0      -1.241 -10.617   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -3.051  -8.125   0.000  0.00  0.00           O-1
HETATM    6  O   UNK     0      -3.392 -10.276   0.000  0.00  0.00           O+0
HETATM    7  P   UNK     0      -3.231 -11.808   0.000  0.00  0.00           P+0
HETATM    8  O   UNK     0      -1.699 -11.647   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -4.762 -11.969   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0      -3.070 -13.339   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0      -4.316 -14.245   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      -5.561 -15.150   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -3.410 -15.491   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0      -5.221 -12.999   0.000  0.00  0.00           O-1
HETATM   15  C   UNK     0       0.185  -6.029   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.185  -4.489   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.555  -5.259   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.095  -5.259   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       1.650  -6.505   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.126  -7.970   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0       1.095  -9.114   0.000  0.00  0.00           P+0
HETATM   23  O   UNK     0       0.065 -10.259   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -0.049  -8.084   0.000  0.00  0.00           O-1
HETATM   25  O   UNK     0       2.240 -10.145   0.000  0.00  0.00           O+0
HETATM   26  P   UNK     0       1.919 -11.651   0.000  0.00  0.00           P+0
HETATM   27  O   UNK     0       0.413 -11.331   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       3.426 -11.971   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       1.599 -13.157   0.000  0.00  0.00           O-1
HETATM   30  N   UNK     0       2.126  -2.549   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       4.924   1.777   0.000  0.00  0.00           O+0
HETATM   36  N   UNK     0       6.258  -0.533   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   38  N   UNK     0       7.591  -2.843   0.000  0.00  0.00           N+0
HETATM   39  N   UNK     0       4.924  -2.843   0.000  0.00  0.00           N+0
HETATM   40  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2   15                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3    7                                                       
CONECT    7    6    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    7   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
CONECT   15    1   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   30                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   15                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   24   25                                             
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   22   26                                                       
CONECT   26   25   27   28   29                                             
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   26                                                            
CONECT   30   17   31   40                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34   40                                                  
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40                                                       
CONECT   40   39   33   30                                                  
MASTER        0    0    0    0    0    0    0    0   40    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₀H₁₂N₅O₂₀P₅

Average Mass

677.0930 Da

Monoisotopic Mass

676.87966 Da

IUPAC Name

hydrogen {[5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-4-hydroxy-2-({[oxido({[oxido(phosphonatooxy)phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-3-yl phosphonato]oxy}phosphonate

Traditional Name

hydrogen [5-(2-amino-6-oxo-1H-purin-9-yl)-4-hydroxy-2-({[oxido([oxido(phosphonatooxy)phosphoryl]oxy)phosphoryl]oxy}methyl)oxolan-3-yl phosphonato]oxyphosphonate

CAS Registry Number

Not Available

SMILES

NC1=NC2=C(N=CN2C2OC(COP([O-])(=O)OP([O-])(=O)OP([O-])([O-])=O)C(OP([O-])(=O)OP(O)([O-])=O)C2O)C(=O)N1

InChI Identifier

InChI=1/C10H18N5O20P5/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(32-39(26,27)33-36(18,19)20)3(31-9)1-30-38(24,25)35-40(28,29)34-37(21,22)23/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H,28,29)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/p-6

InChI Key

KCPMACXZAITQAX-UHFFFAOYNA-H

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Classification

Not classified

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	-4.2	ChemAxon
pKa (Strongest Acidic)	0.84	ChemAxon
Physiological Charge	-6	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	404.85 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	112.26 m³·mol⁻¹	ChemAxon
Polarizability	46.56 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Guanosine pentaphosphate

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for pppGpp (NP0339939)

MOL for NP0339939 (pppGpp)

3D MOL for NP0339939 (pppGpp)

3D SDF for NP0339939 (pppGpp)

3D-SDF for NP0339939 (pppGpp)

PDB for NP0339939 (pppGpp)

3D PDB for NP0339939 (pppGpp)

SMILES for NP0339939 (pppGpp)

INCHI for NP0339939 (pppGpp)

Structure for NP0339939 (pppGpp)

3D Structure for NP0339939 (pppGpp)