NP-MRD: Showing NP-Card for (2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol (NP0191704)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-04 08:44:40 UTC

Updated at

2022-09-04 08:44:40 UTC

NP-MRD ID

NP0191704

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol

Description

(2R,3R,4S,5R)-2-{4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-5-(hydroxymethyl)oxolane-3,4-diol belongs to the class of organic compounds known as pyrrolopyrimidine nucleosides and nucleotides. These are nucleoside derivatives containing a ribose derivative which is n-glycosylated to a pyrrolopyrimidine. Also called deazapurine nucleosides, they are analogs of purine nucleosides with the N atom of the purine being replaced by a C atom at position 7. Based on a literature review very few articles have been published on (2R,3R,4S,5R)-2-{4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-5-(hydroxymethyl)oxolane-3,4-diol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 34  0  0  0  0  0  0  0  0999 V2000
   -3.2732   -1.1492    1.8631 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5446    0.1021    1.3414 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4967    0.5228    0.3570 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2170    0.5874    0.9349 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4586    0.9128   -0.2123 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9564    0.8269    0.0388 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7759    1.8865    0.2004 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0710    1.4733    0.4253 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0294    0.0897    0.3977 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0257   -0.8533    0.5616 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3234   -0.4270    0.7993 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6914   -2.1506    0.4830 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4048   -2.4860    0.2487 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4283   -1.5688    0.0879 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7192   -0.2609    0.1589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9378    0.0042   -1.3001 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2628    0.7601   -2.4487 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2636   -0.4926   -0.7299 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2430   -0.4664   -1.7069 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1250   -1.5138    2.2646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5013    0.8212    2.1958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5247    0.2066    0.8809 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7193    1.4850   -0.0930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7472    1.9529   -0.4676 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4625    2.9195    0.1596 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9636    2.0847    0.5935 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8354    0.1440    0.1258 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1811   -3.5336    0.1935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2593   -0.8224   -1.5380 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0750    1.7320   -2.2910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0850   -1.5125   -0.3438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1339   -1.2745   -2.2672 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 18  3  1  0
 15  6  1  0
 15  9  1  0
  1 20  1  0
  2 21  1  0
  2 22  1  0
  3 23  1  6
  5 24  1  6
 16 29  1  6
 17 30  1  0
 18 31  1  1
 19 32  1  0
  7 25  1  0
  8 26  1  0
 11 27  1  0
 13 28  1  0
M  END


  Mrv1652309042210442D          

 19 21  0  0  1  0            999 V2000
   -0.4820   -4.5353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -3.2299    0.0000 C   0  0  1  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  1  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 C   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
    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
    1.3687   -2.8174    0.0000 C   0  0  2  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  2  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
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 10 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
  9 15  1  0  0  0  0
  6 15  1  0  0  0  0
  5 16  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
  3 18  1  0  0  0  0
 18 19  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0191704

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC2=C(O)N=CN=C12

> <INCHI_IDENTIFIER>
InChI=1S/C11H13N3O5/c15-3-6-7(16)8(17)11(19-6)14-2-1-5-9(14)12-4-13-10(5)18/h1-2,4,6-8,11,15-17H,3H2,(H,12,13,18)/t6-,7-,8-,11-/m1/s1

> <INCHI_KEY>
DPRSKJHWKNHBOW-KCGFPETGSA-N

> <FORMULA>
C11H13N3O5

> <MOLECULAR_WEIGHT>
267.241

> <EXACT_MASS>
267.085520531

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
25.11461172022627

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R)-2-{4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-5-(hydroxymethyl)oxolane-3,4-diol

> <JCHEM_LOGP>
-0.7530994293333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.913755663123826

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.285944896791245

> <JCHEM_PKA_STRONGEST_BASIC>
2.1800285936352255

> <JCHEM_POLAR_SURFACE_AREA>
120.86000000000001

> <JCHEM_REFRACTIVITY>
62.6521

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  O   UNK     0      -0.900  -8.466   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.061  -6.934   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.185  -6.029   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.185  -4.489   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       2.126  -2.549   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.126  -0.057   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.924   1.777   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       6.258  -0.533   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       4.924  -2.843   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.555  -5.259   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.095  -5.259   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       1.650  -6.505   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       2.126  -7.970   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   18                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   16                                                  
CONECT    6    5    7   15                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   15                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14    9    6                                                  
CONECT   16    5   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    3   19                                                  
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₃N₃O₅

Average Mass

267.2410 Da

Monoisotopic Mass

267.08552 Da

IUPAC Name

(2R,3R,4S,5R)-2-{4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-5-(hydroxymethyl)oxolane-3,4-diol

Traditional Name

(2R,3S,4R,5R)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC2=C(O)N=CN=C12

InChI Identifier

InChI=1S/C11H13N3O5/c15-3-6-7(16)8(17)11(19-6)14-2-1-5-9(14)12-4-13-10(5)18/h1-2,4,6-8,11,15-17H,3H2,(H,12,13,18)/t6-,7-,8-,11-/m1/s1

InChI Key

DPRSKJHWKNHBOW-KCGFPETGSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrrolopyrimidine nucleosides and nucleotides. These are nucleoside derivatives containing a ribose derivative which is n-glycosylated to a pyrrolopyrimidine. Also called deazapurine nucleosides, they are analogs of purine nucleosides with the N atom of the purine being replaced by a C atom at position 7.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrrolopyrimidine nucleosides and nucleotides

Sub Class

Not Available

Direct Parent

Pyrrolopyrimidine nucleosides and nucleotides

Alternative Parents

Substituents

Pyrrolopyrimidine ribonucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Pyrrolo[2,3-d]pyrimidine
Pyrrolopyrimidine
Pyrimidone
Monosaccharide
Pyrimidine
Substituted pyrrole
Vinylogous amide
Heteroaromatic compound
Tetrahydrofuran
Pyrrole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Primary alcohol
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Alcohol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	-0.75	ChemAxon
pKa (Strongest Acidic)	12.29	ChemAxon
pKa (Strongest Basic)	2.18	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	120.86 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	62.65 m³·mol⁻¹	ChemAxon
Polarizability	25.11 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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

87646

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

97094

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol (NP0191704)

MOL for NP0191704 ((2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol)

3D MOL for NP0191704 ((2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol)

3D SDF for NP0191704 ((2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol)

3D-SDF for NP0191704 ((2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol)

PDB for NP0191704 ((2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol)

3D PDB for NP0191704 ((2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol)

SMILES for NP0191704 ((2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol)

INCHI for NP0191704 ((2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol)

Structure for NP0191704 ((2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol)

3D Structure for NP0191704 ((2r,3s,4r,5r)-2-(hydroxymethyl)-5-{4-hydroxypyrrolo[2,3-d]pyrimidin-7-yl}oxolane-3,4-diol)