NP-MRD: Showing NP-Card for Ribocitrin (NP0062107)

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Record Information

Version

2.0

Created at

2022-04-28 06:46:30 UTC

Updated at

2022-04-28 06:46:30 UTC

NP-MRD ID

NP0062107

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Ribocitrin

Description

(2R)-2-{[(2S,3S,4R,5R)-4-{[(2R,3R,4R,5R)-3-{[(2S,3S,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}butane-1,2,4-tricarboxylic acid belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. Ribocitrin is found in Streptomyces sp. MF980-CF1. Based on a literature review very few articles have been published on (2R)-2-{[(2S,3S,4R,5R)-4-{[(2R,3R,4R,5R)-3-{[(2S,3S,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}butane-1,2,4-tricarboxylic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208462D          

 41 43  0  0  1  0            999 V2000
    3.2475   -2.0622    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8350   -1.3477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  6  0  0  0
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  1 14  1  1  0  0  0
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 15 40  1  0  0  0  0
 16 41  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282208462D          

 41 43  0  0  1  0            999 V2000
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   -1.0175   -9.0855    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3980   -7.6655    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2185   -7.7517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5540   -8.5054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9855   -6.9510    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6222   -8.3555    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9455   -4.5692    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4304   -5.2367    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2509   -5.1504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2004   -3.7846    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0809   -3.5297    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  1  9  1  0  0  0  0
  9 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
  1 14  1  1  0  0  0
 15 14  1  6  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  6  0  0  0
 19 18  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  6  0  0  0
 21 23  1  0  0  0  0
 23 24  1  1  0  0  0
 24 25  1  0  0  0  0
 23 26  1  0  0  0  0
 19 26  1  0  0  0  0
 20 27  1  6  0  0  0
 28 27  1  1  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  1  0  0  0
 30 32  1  0  0  0  0
 32 33  1  1  0  0  0
 33 34  1  0  0  0  0
 32 35  1  0  0  0  0
 28 35  1  0  0  0  0
 29 36  1  1  0  0  0
 17 37  1  0  0  0  0
 37 38  1  6  0  0  0
 38 39  1  0  0  0  0
 37 40  1  0  0  0  0
 15 40  1  0  0  0  0
 16 41  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0062107

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](O[C@@H]2[C@H](O)[C@@H](CO)O[C@@H]2O[C@@H]2[C@H](O)[C@H](O[C@](CCC(O)=O)(CC(O)=O)C(O)=O)O[C@@H]2CO)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C22H34O19/c23-4-7-12(30)14(32)18(36-7)40-17-13(31)8(5-24)37-20(17)39-16-9(6-25)38-19(15(16)33)41-22(21(34)35,3-11(28)29)2-1-10(26)27/h7-9,12-20,23-25,30-33H,1-6H2,(H,26,27)(H,28,29)(H,34,35)/t7-,8-,9-,12+,13-,14+,15+,16+,17-,18+,19+,20-,22-/m1/s1

> <INCHI_KEY>
RGAMJCJDWKLDHT-RFSHGXQCSA-N

> <FORMULA>
C22H34O19

> <MOLECULAR_WEIGHT>
602.495

> <EXACT_MASS>
602.169428875

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
55.24426916213048

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-{[(2S,3S,4R,5R)-4-{[(2R,3R,4R,5R)-3-{[(2S,3S,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}butane-1,2,4-tricarboxylic acid

> <ALOGPS_LOGP>
-1.52

> <JCHEM_LOGP>
-4.455528358

> <ALOGPS_LOGS>
-0.46

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.7903633783378154

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9885902680849163

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981438436558344

> <JCHEM_POLAR_SURFACE_AREA>
308.89

> <JCHEM_REFRACTIVITY>
119.73129999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.10e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-{[(2S,3S,4R,5R)-4-{[(2R,3R,4R,5R)-3-{[(2S,3S,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}butane-1,2,4-tricarboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       6.062  -3.849   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.292  -2.516   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.752  -2.516   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       6.062  -1.182   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.396  -3.079   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.396  -1.539   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.729  -0.769   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       6.365  -0.395   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       6.832  -5.183   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.372  -5.183   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.142  -6.517   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      10.682  -6.517   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       8.372  -7.850   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       4.728  -4.619   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       4.728  -6.159   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.482  -7.065   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.958  -8.529   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.053  -9.775   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.521  -9.614   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.491 -10.759   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.916 -10.132   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -2.250 -10.902   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.755  -8.601   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.899  -7.570   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -1.579  -6.064   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.751  -8.280   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.811 -12.265   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -0.333 -13.295   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.172 -14.827   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.579 -15.453   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -1.899 -16.960   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -2.610 -14.309   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -4.141 -14.470   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -4.768 -15.877   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -1.840 -12.975   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       1.161 -15.597   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       5.498  -8.529   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       6.403  -9.775   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       7.935  -9.614   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       5.974  -7.065   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       2.018  -6.589   0.000  0.00  0.00           O+0
CONECT    1    2    5    9   14                                             
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    1    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    1   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    1   15                                                       
CONECT   15   14   16   40                                                  
CONECT   16   15   17   41                                                  
CONECT   17   16   18   37                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   26                                                  
CONECT   20   19   21   27                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24                                                            
CONECT   26   23   19                                                       
CONECT   27   20   28                                                       
CONECT   28   27   29   35                                                  
CONECT   29   28   30   36                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   35                                                  
CONECT   33   32   34                                                       
CONECT   34   33                                                            
CONECT   35   32   28                                                       
CONECT   36   29                                                            
CONECT   37   17   38   40                                                  
CONECT   38   37   39                                                       
CONECT   39   38                                                            
CONECT   40   37   15                                                       
CONECT   41   16                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   86    0
END

View in JSmol

Synonyms

Value	Source
(2R)-2-{[(2S,3S,4R,5R)-4-{[(2R,3R,4R,5R)-3-{[(2S,3S,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}butane-1,2,4-tricarboxylate	Generator

Chemical Formula

C₂₂H₃₄O₁₉

Average Mass

602.4950 Da

Monoisotopic Mass

602.16943 Da

IUPAC Name

Traditional Name

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](O[C@@H]2[C@H](O)[C@@H](CO)O[C@@H]2O[C@@H]2[C@H](O)[C@H](O[C@](CCC(O)=O)(CC(O)=O)C(O)=O)O[C@@H]2CO)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C22H34O19/c23-4-7-12(30)14(32)18(36-7)40-17-13(31)8(5-24)37-20(17)39-16-9(6-25)38-19(15(16)33)41-22(21(34)35,3-11(28)29)2-1-10(26)27/h7-9,12-20,23-25,30-33H,1-6H2,(H,26,27)(H,28,29)(H,34,35)/t7-,8-,9-,12+,13-,14+,15+,16+,17-,18+,19+,20-,22-/m1/s1

InChI Key

RGAMJCJDWKLDHT-RFSHGXQCSA-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
Streptomyces sp. MF980-CF1	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

O-glycosyl compound
Disaccharide
Tricarboxylic acid or derivatives
Tetrahydrofuran
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Carboxylic acid
Carboxylic acid derivative
Acetal
Organic oxide
Hydrocarbon derivative
Primary alcohol
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	-1.5	ALOGPS
logP	-4.5	ChemAxon
logS	-0.46	ALOGPS
pKa (Strongest Acidic)	2.99	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	308.89 Å²	ChemAxon
Rotatable Bond Count	15	ChemAxon
Refractivity	119.73 m³·mol⁻¹	ChemAxon
Polarizability	55.24 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

Not Available

METLIN ID

Not Available

PubChem Compound

162897715

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Ribocitrin (NP0062107)

MOL for NP0062107 (Ribocitrin)

3D MOL for NP0062107 (Ribocitrin)

3D SDF for NP0062107 (Ribocitrin)

3D-SDF for NP0062107 (Ribocitrin)

PDB for NP0062107 (Ribocitrin)

3D PDB for NP0062107 (Ribocitrin)

SMILES for NP0062107 (Ribocitrin)

INCHI for NP0062107 (Ribocitrin)

Structure for NP0062107 (Ribocitrin)

3D Structure for NP0062107 (Ribocitrin)