NP-MRD: Showing NP-Card for N5-Carboxyaminoimidazole ribonucleotide (NP0092005)

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Record Information

Version

2.0

Created at

2022-05-11 18:54:31 UTC

Updated at

2022-05-11 18:54:31 UTC

NP-MRD ID

NP0092005

Secondary Accession Numbers

None

Natural Product Identification

Common Name

N5-Carboxyaminoimidazole ribonucleotide

Description

N5-Carboxyaminoimidazole ribonucleotide belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups. N5-Carboxyaminoimidazole ribonucleotide is a very strong basic compound (based on its pKa). N5-Carboxyaminoimidazole ribonucleotide exists in all eukaryotes, ranging from yeast to humans. The de novo biosynthetic pathway for purine nucleotides is highly conserved among organisms, but its regulation and the organization of the genes encoding the enzymes vary.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 37  0  0  0  0  0  0  0  0999 V2000
    4.7752    2.1498   -0.9506 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6413    2.3283   -0.4489 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2795    3.6693   -0.2594 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7399    1.3031   -0.0768 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0269   -0.0833   -0.2346 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1653   -0.6626   -0.7474 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9894   -1.9928   -0.7007 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7878   -2.2325   -0.1789 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1854   -1.0812    0.1118 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8667   -0.9833    0.6928 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1067    0.0176    0.1008 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1669   -0.1988    0.6051 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2506    0.3461   -0.2630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1517    1.7281   -0.4508 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4634    2.1537   -1.4579 P   0  0  1  0  0  5  0  0  0  0  0  0
   -3.2298    1.6628   -2.8479 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8377    1.3953   -0.7983 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7209    3.8077   -1.4746 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3523   -1.6860    0.7242 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3070   -2.1823   -0.1565 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0376   -2.2146    0.3899 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3736   -3.2905    1.2081 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3300    3.9577   -0.1168 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8218    1.5889    0.3326 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0498   -0.1250   -1.1233 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3642   -3.2396   -0.0161 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8660   -0.8436    1.7793 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2562    0.2713    1.6118 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2920   -0.1681   -1.2442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2179    0.1592    0.2338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8652    1.6897    0.1663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0243    4.1661   -0.6037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5556   -1.9922    1.7729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9511   -2.8021    0.2765 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1011   -2.5089   -0.6819 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1342   -4.1075    0.7012 H   0  0  0  0  0  0  0  0  0  0  0  0
 20 19  1  0
 19 12  1  0
 12 13  1  0
 13 14  1  0
 15 14  1  1
 15 17  1  0
 15 18  1  0
 15 16  2  0
 12 11  1  0
 11 10  1  0
 10 21  1  0
 21 22  1  0
 10  9  1  0
  9  8  1  0
  8  7  2  0
  7  6  1  0
  6  5  2  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
 21 19  1  0
  5  9  1  0
 20 34  1  0
 19 33  1  1
 12 28  1  1
 13 29  1  0
 13 30  1  0
 17 31  1  0
 18 32  1  0
 10 27  1  1
 21 35  1  6
 22 36  1  0
  8 26  1  0
  6 25  1  0
  4 24  1  0
  3 23  1  0
M  END


  Mrv0541 02241203542D          

 22 23  0  0  0  0            999 V2000
   15.0263   -9.8191    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4795  -11.7965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0263  -11.1539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3045  -11.7965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2417  -10.0740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7895  -12.4640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5742  -12.2090    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5742  -11.3840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8439   -9.7769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5107  -10.4864    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.6286   -9.5220    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.2417  -10.8989    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.5346  -13.2486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2417  -12.6940    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6724  -10.5839    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2308   -9.2249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2421  -11.6861    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2421  -13.3360    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4171  -12.5110    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0670  -12.5110    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7895  -11.1291    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2421  -12.5110    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  1  5  2  0  0  0  0
  2  4  1  0  0  0  0
  2 20  1  0  0  0  0
  3 12  1  0  0  0  0
  3 10  2  0  0  0  0
  4  6  1  0  0  0  0
  4 21  1  0  0  0  0
  5 12  1  0  0  0  0
  5 11  1  0  0  0  0
  6 13  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7 14  1  0  0  0  0
  8 21  1  0  0  0  0
  8 12  1  0  0  0  0
  9 11  1  0  0  0  0
  9 15  1  0  0  0  0
  9 16  2  0  0  0  0
 17 22  1  0  0  0  0
 18 22  1  0  0  0  0
 19 22  2  0  0  0  0
 20 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0092005

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1C(COP(O)(O)=O)OC(C1O)N1C=NC=C1NC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N3O9P/c13-6-4(2-20-22(17,18)19)21-8(7(6)14)12-3-10-1-5(12)11-9(15)16/h1,3-4,6-8,11,13-14H,2H2,(H,15,16)(H2,17,18,19)

> <INCHI_KEY>
JHLXDWGVSYMXPL-UHFFFAOYSA-N

> <FORMULA>
C9H14N3O9P

> <MOLECULAR_WEIGHT>
339.1959

> <EXACT_MASS>
339.046765573

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
28.38011029681859

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1-{3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl}-1H-imidazol-5-yl)carbamic acid

> <ALOGPS_LOGP>
-2.13

> <JCHEM_LOGP>
-3.4212731610733864

> <ALOGPS_LOGS>
-2.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.2551828758389445

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1822089997363596

> <JCHEM_PKA_STRONGEST_BASIC>
5.825351746342738

> <JCHEM_POLAR_SURFACE_AREA>
183.6

> <JCHEM_REFRACTIVITY>
67.4528

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.61e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl}imidazol-4-ylcarbamic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      28.049 -18.329   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      21.428 -22.020   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      28.049 -20.821   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      22.968 -22.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      26.585 -18.805   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      23.874 -23.266   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      25.339 -22.790   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      25.339 -21.250   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      23.975 -18.250   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      28.953 -19.575   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0      25.440 -17.774   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      26.585 -20.345   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0      23.398 -24.731   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      26.585 -23.695   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      23.655 -19.757   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      22.831 -17.220   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      19.119 -21.814   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      19.119 -24.894   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      17.579 -23.354   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      20.658 -23.354   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      23.874 -20.774   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0      19.119 -23.354   0.000  0.00  0.00           P+0
CONECT    1   10    5                                                       
CONECT    2    4   20                                                       
CONECT    3   12   10                                                       
CONECT    4    2    6   21                                                  
CONECT    5    1   12   11                                                  
CONECT    6    4   13    7                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7   21   12                                                  
CONECT    9   11   15   16                                                  
CONECT   10    1    3                                                       
CONECT   11    5    9                                                       
CONECT   12    3    5    8                                                  
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    9                                                            
CONECT   16    9                                                            
CONECT   17   22                                                            
CONECT   18   22                                                            
CONECT   19   22                                                            
CONECT   20    2   22                                                       
CONECT   21    4    8                                                       
CONECT   22   17   18   19   20                                             
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₁₄N₃O₉P

Average Mass

339.1959 Da

Monoisotopic Mass

339.04677 Da

IUPAC Name

(1-{3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl}-1H-imidazol-5-yl)carbamic acid

Traditional Name

3-{3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl}imidazol-4-ylcarbamic acid

CAS Registry Number

Not Available

SMILES

OC1C(COP(O)(O)=O)OC(C1O)N1C=NC=C1NC(O)=O

InChI Identifier

InChI=1S/C9H14N3O9P/c13-6-4(2-20-22(17,18)19)21-8(7(6)14)12-3-10-1-5(12)11-9(15)16/h1,3-4,6-8,11,13-14H,2H2,(H,15,16)(H2,17,18,19)

InChI Key

JHLXDWGVSYMXPL-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
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
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
Imidazole ribonucleoside
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Monoalkyl phosphate
N-substituted imidazole
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Azole
Tetrahydrofuran
Imidazole
Heteroaromatic compound
1,2-diol
Secondary alcohol
Carbamic acid
Carbamic acid derivative
Carbonic acid derivative
Oxacycle
Azacycle
Organoheterocyclic compound
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Carbonyl group
Hydrocarbon derivative
Alcohol
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	-2.1	ALOGPS
logP	-3.4	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	1.18	ChemAxon
pKa (Strongest Basic)	5.83	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	183.6 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	67.45 m³·mol⁻¹	ChemAxon
Polarizability	28.38 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0012268

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB028906

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

CPD0-181

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25201011

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for N5-Carboxyaminoimidazole ribonucleotide (NP0092005)

MOL for NP0092005 (N5-Carboxyaminoimidazole ribonucleotide)

3D MOL for NP0092005 (N5-Carboxyaminoimidazole ribonucleotide)

3D SDF for NP0092005 (N5-Carboxyaminoimidazole ribonucleotide)

3D-SDF for NP0092005 (N5-Carboxyaminoimidazole ribonucleotide)

PDB for NP0092005 (N5-Carboxyaminoimidazole ribonucleotide)

3D PDB for NP0092005 (N5-Carboxyaminoimidazole ribonucleotide)

SMILES for NP0092005 (N5-Carboxyaminoimidazole ribonucleotide)

INCHI for NP0092005 (N5-Carboxyaminoimidazole ribonucleotide)

Structure for NP0092005 (N5-Carboxyaminoimidazole ribonucleotide)

3D Structure for NP0092005 (N5-Carboxyaminoimidazole ribonucleotide)