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Showing NP-Card for Glycineamideribotide (NP0334696)

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Record Information
Version2.0
Created at2024-09-10 19:33:56 UTC
Updated at2024-09-10 19:33:56 UTC
NP-MRD IDNP0334696
Secondary Accession NumbersNone
Natural Product Identification
Common NameGlycineamideribotide
DescriptionGlycineamideribotide belongs to the class of organic compounds known as glycinamide ribonucleotides. Glycinamide ribonucleotides are compounds in which the amide N atom of glycineamide is linked to the C-1 of a ribosyl (or deoxyribosyl) moiety. Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) moiety. Based on a literature review very few articles have been published on Glycineamideribotide.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0334696 (Glycineamideribotide)


  Mrv2104 05252322062D          

 18 18  0  0  0  0            999 V2000
10001.391910000.5628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.106710000.1508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.819410000.5628    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10002.409510001.2755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.534210000.1508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.233410001.2755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.8852 9998.7044    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.627810000.5628    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9999.0941 9998.7126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.913810000.1508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.199910000.5628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.9138 9999.3263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.485710000.1508    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10000.006310000.6450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.338910000.1600    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.5938 9999.3754    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.4188 9999.3754    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.673710000.1600    0.0000 C   0  0  1  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
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
 11 13  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
 14 15  1  0  0  0  0
 14 18  1  0  0  0  0
 18  1  1  6  0  0  0
 17  7  1  1  0  0  0
 15  8  1  6  0  0  0
 16  9  1  1  0  0  0
M  END
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3D MOL for NP0334696 (Glycineamideribotide)

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3D SDF for NP0334696 (Glycineamideribotide)

  Mrv2104 05252322062D          

 18 18  0  0  0  0            999 V2000
10001.391910000.5628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.106710000.1508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.819410000.5628    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10002.409510001.2755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.534210000.1508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.233410001.2755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.8852 9998.7044    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.627810000.5628    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9999.0941 9998.7126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.913810000.1508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.199910000.5628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.9138 9999.3263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.485710000.1508    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10000.006310000.6450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.338910000.1600    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.5938 9999.3754    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.4188 9999.3754    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.673710000.1600    0.0000 C   0  0  1  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
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
 11 13  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
 14 15  1  0  0  0  0
 14 18  1  0  0  0  0
 18  1  1  6  0  0  0
 17  7  1  1  0  0  0
 15  8  1  6  0  0  0
 16  9  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0334696

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCC(=O)N[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/t3-,5-,6-,7-/s2

> <INCHI_KEY>
OBQMLSFOUZUIOB-VVXDDPDLNA-N

> <FORMULA>
C7H15N2O8P

> <MOLECULAR_WEIGHT>
286.177

> <EXACT_MASS>
286.056602449

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
23.698343293865314

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-(2-aminoacetamido)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

> <JCHEM_LOGP>
-4.650616976017661

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.245768050847792

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2255744528280512

> <JCHEM_PKA_STRONGEST_BASIC>
8.141960108603826

> <JCHEM_POLAR_SURFACE_AREA>
171.57000000000002

> <JCHEM_REFRACTIVITY>
55.2948

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
glycineamide ribonucleotide

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0334696 (Glycineamideribotide)
Download
PDB for NP0334696 (Glycineamideribotide)
HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  C   UNK     0    8669.2658667.717   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8670.5998666.948   0.000  0.00  0.00           O+0
HETATM    3  P   UNK     0    8671.9308667.717   0.000  0.00  0.00           P+0
HETATM    4  O   UNK     0    8671.1648669.048   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8673.2648666.948   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8672.7028669.048   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8668.3198664.248   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0    8664.1058667.717   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0    8664.9768664.264   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0    8662.7728666.948   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8661.4408667.717   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0    8662.7728665.409   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0    8660.1078666.948   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0    8666.6788667.871   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0    8665.4338666.965   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8665.9088665.501   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8667.4488665.501   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8667.9248666.965   0.000  0.00  0.00           C+0
CONECT    1    2   18                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3                                                            
CONECT    7   17                                                            
CONECT    8   10   15                                                       
CONECT    9   16                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10   13                                                       
CONECT   12   10                                                            
CONECT   13   11                                                            
CONECT   14   15   18                                                       
CONECT   15   16   14    8                                                  
CONECT   16   15   17    9                                                  
CONECT   17   16   18    7                                                  
CONECT   18   17   14    1                                                  
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

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3D PDB for NP0334696 (Glycineamideribotide)
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SMILES for NP0334696 (Glycineamideribotide)
NCC(=O)N[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O
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INCHI for NP0334696 (Glycineamideribotide)
InChI=1/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/t3-,5-,6-,7-/s2
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View in JSmol
SynonymsNot Available
Chemical FormulaC7H15N2O8P
Average Mass286.1770 Da
Monoisotopic Mass286.05660 Da
IUPAC Name{[(2R,3S,4R,5R)-5-(2-aminoacetamido)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional Nameglycineamide ribonucleotide
CAS Registry NumberNot Available
SMILES
NCC(=O)N[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O
InChI Identifier
InChI=1/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/t3-,5-,6-,7-/s2
InChI KeyOBQMLSFOUZUIOB-VVXDDPDLNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as glycinamide ribonucleotides. These are compounds in which the amide N atom of glycineamide is linked to the C-1 of a ribosyl (or deoxyribosyl) moiety. Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) moiety.
KingdomOrganic compounds  
Super ClassNucleosides, nucleotides, and analogues  
ClassGlycinamide ribonucleotides  
Sub ClassNot Available
Direct ParentGlycinamide ribonucleotides  
Alternative Parents
Substituents
  • Glycinamide-ribonucleotide
    • 

  • Pentose phosphate
    • 

  • Pentose-5-phosphate
    • 

  • Alpha-amino acid amide
    • 

  • Alpha-amino acid or derivatives
    • 

  • Monosaccharide phosphate
    • 

  • Pentose monosaccharide
    • 

  • Monoalkyl phosphate
    • 

  • Monosaccharide
    • 

  • Organic phosphoric acid derivative
    • 

  • Phosphoric acid ester
    • 

  • Alkyl phosphate
    • 

  • Tetrahydrofuran
    • 

  • Secondary carboxylic acid amide
    • 

  • Secondary alcohol
    • 

  • Amino acid or derivatives
    • 

  • Carboxamide group
    • 

  • 1,2-diol
    • 

  • Organoheterocyclic compound
    • 

  • Oxacycle
    • 

  • Carboxylic acid derivative
    • 

  • Organic nitrogen compound
    • 

  • Organic oxide
    • 

  • Primary aliphatic amine
    • 

  • Organopnictogen compound
    • 

  • Alcohol
    • 

  • Organonitrogen compound
    • 

  • Carbonyl group
    • 

  • Organooxygen compound
    • 

  • Amine
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-4.7ChemAxon
pKa (Strongest Acidic)1.23ChemAxon
pKa (Strongest Basic)8.14ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area171.57 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity55.29 m³·mol⁻¹ChemAxon
Polarizability23.7 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00007395  
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGlycineamide ribonucleotide  
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available