NP-MRD: Showing NP-Card for N6-succinoadenosine (NP0332128)

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Record Information

Version

2.0

Created at

2023-11-22 20:00:29 UTC

Updated at

2025-02-11 15:44:19 UTC

NP-MRD ID

NP0332128

Natural Product DOI

https://doi.org/10.57994/1285

Secondary Accession Numbers

None

Natural Product Identification

Common Name

N6-succinoadenosine

Description

Based on a literature review very few articles have been published on 2-({9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)butanedioic acid.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 11222320002D          

 28 30  0  0  1  0            999 V2000
   -1.7772    5.3471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1097    5.8320    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3251    5.5771    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1598    6.2445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3251    6.9119    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1097    6.6570    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7772    7.1419    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0702    7.6966    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7368    7.8681    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9085    4.9937    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0702    4.7924    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0702    3.4576    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5551    4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  6  0  0  0
  5  8  1  1  0  0  0
  8  9  1  0  0  0  0
  3 10  1  6  0  0  0
  3 11  1  1  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  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
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
 18 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  2  0  0  0  0
 16 26  2  0  0  0  0
 12 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 11 28  1  0  0  0  0
M  END


  Mrv2104 11222320002D          

 28 30  0  0  1  0            999 V2000
   -1.7772    5.3471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1097    5.8320    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3251    5.5771    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1598    6.2445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3251    6.9119    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1097    6.6570    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7772    7.1419    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0702    7.6966    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7368    7.8681    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9085    4.9937    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0702    4.7924    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0702    3.4576    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5551    4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  6  0  0  0
  5  8  1  1  0  0  0
  8  9  1  0  0  0  0
  3 10  1  6  0  0  0
  3 11  1  1  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  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
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
 18 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  2  0  0  0  0
 16 26  2  0  0  0  0
 12 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 11 28  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332128

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]1(O[C@H](CO)[C@@H](O)[C@H]1O)N1C=NC2=C(NC(CC(O)=O)C(O)=O)N=CN=C12

> <INCHI_IDENTIFIER>
InChI=1S/C14H17N5O8/c20-2-6-9(23)10(24)13(27-6)19-4-17-8-11(15-3-16-12(8)19)18-5(14(25)26)1-7(21)22/h3-6,9-10,13,20,23-24H,1-2H2,(H,21,22)(H,25,26)(H,15,16,18)/t5?,6-,9-,10-,13-/m1/s1

> <INCHI_KEY>
VKGZCEJTCKHMRL-DPXQIYNJSA-N

> <FORMULA>
C14H17N5O8

> <MOLECULAR_WEIGHT>
383.317

> <EXACT_MASS>
383.107712527

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
35.270783188663515

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-({9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-9H-purin-6-yl}amino)butanedioic acid

> <JCHEM_LOGP>
-3.337375831505995

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.125719591292181

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9990481259765227

> <JCHEM_PKA_STRONGEST_BASIC>
3.6293703006322704

> <JCHEM_POLAR_SURFACE_AREA>
200.14999999999998

> <JCHEM_REFRACTIVITY>
85.30289999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-({9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)butanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-NOV-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-NOV-23         0                                  
HETATM    1  O   UNK     0      -3.317   9.981   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.071  10.886   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.607  10.411   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.298  11.656   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -0.607  12.902   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.071  12.426   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.317  13.332   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -0.131  14.367   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.375  14.687   0.000  0.00  0.00           O+0
HETATM   10  H   UNK     0      -1.696   9.322   0.000  0.00  0.00           H+0
HETATM   11  N   UNK     0      -0.131   8.946   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       1.334   8.470   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       2.667   9.240   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       4.001   6.930   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       2.667   4.620   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       8.002   4.620   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       6.668   2.310   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      -0.131   6.454   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0      -1.036   7.700   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4   10   11                                             
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    2    7                                                  
CONECT    7    6                                                            
CONECT    8    5    9                                                       
CONECT    9    8                                                            
CONECT   10    3                                                            
CONECT   11    3   12   28                                                  
CONECT   12   11   13   26                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   26                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   22                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
CONECT   22   18   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   16   12   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27   11                                                       
MASTER        0    0    0    0    0    0    0    0   28    0   60    0
END

View in JSmol

Synonyms

Value	Source
2-({9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)butanedioate	Generator

Chemical Formula

C₁₄H₁₇N₅O₈

Average Mass

383.3170 Da

Monoisotopic Mass

383.10771 Da

IUPAC Name

2-({9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-9H-purin-6-yl}amino)butanedioic acid

Traditional Name

2-({9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purin-6-yl}amino)butanedioic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(O[C@H](CO)[C@@H](O)[C@H]1O)N1C=NC2=C(NC(CC(O)=O)C(O)=O)N=CN=C12

InChI Identifier

InChI=1S/C14H17N5O8/c20-2-6-9(23)10(24)13(27-6)19-4-17-8-11(15-3-16-12(8)19)18-5(14(25)26)1-7(21)22/h3-6,9-10,13,20,23-24H,1-2H2,(H,21,22)(H,25,26)(H,15,16,18)/t5?,6-,9-,10-,13-/m1/s1

InChI Key

VKGZCEJTCKHMRL-DPXQIYNJSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D2O, experimental)	laurence.marcourt@unige.ch	Geneva university	Laurence Marcourt	2024-05-03	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D2O, experimental)	laurence.marcourt@unige.ch	Geneva university	Laurence Marcourt	2024-05-03	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, D2O, experimental)	laurence.marcourt@unige.ch	Geneva university	Laurence Marcourt	2024-05-03	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, D2O, experimental)	laurence.marcourt@unige.ch	Geneva university	Laurence Marcourt	2024-05-03	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, D2O, experimental)	laurence.marcourt@unige.ch	Geneva university	Laurence Marcourt	2024-05-03	View Spectrum
TOCSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, D2O, experimental)	laurence.marcourt@unige.ch	Geneva university	Laurence Marcourt	2024-05-03	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D2O, experimental)	laurence.marcourt@unige.ch	Geneva university	Laurence Marcourt	2024-05-03	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600.17282104, 540 uL of phosphate buffer (203 mM Na2HPO4, 44 mM NaH2PO4 (pH 7.4), 1 mM TSP, 3 mM NaN3) and 60 uL o, simulated)	laurence.marcourt@unige.ch	Geneva university	Laurence Marcourt	2024-05-03	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600.17282104, D₂O, simulated)	laurence.marcourt@unige.ch	Geneva university	Laurence Marcourt	2024-05-03	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Bordeaux Supérieur appellation		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	-3.3	ChemAxon
pKa (Strongest Acidic)	3	ChemAxon
pKa (Strongest Basic)	3.63	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	200.15 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	85.3 m³·mol⁻¹	ChemAxon
Polarizability	35.27 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

20171518

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

20849084

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for N6-succinoadenosine (NP0332128)

MOL for NP0332128 (N6-succinoadenosine)

3D MOL for NP0332128 (N6-succinoadenosine)

3D SDF for NP0332128 (N6-succinoadenosine)

3D-SDF for NP0332128 (N6-succinoadenosine)

PDB for NP0332128 (N6-succinoadenosine)

3D PDB for NP0332128 (N6-succinoadenosine)

SMILES for NP0332128 (N6-succinoadenosine)

INCHI for NP0332128 (N6-succinoadenosine)

Structure for NP0332128 (N6-succinoadenosine)

3D Structure for NP0332128 (N6-succinoadenosine)