NP-MRD: Showing NP-Card for D-Ribulose 1,5-bisphosphate (NP0054909)

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Record Information

Version

2.0

Created at

2022-04-28 01:06:57 UTC

Updated at

2022-04-28 01:06:57 UTC

NP-MRD ID

NP0054909

Secondary Accession Numbers

None

Natural Product Identification

Common Name

D-Ribulose 1,5-bisphosphate

Description

D-Ribulose 1,5-bisphosphate is found in Arabidopsis thaliana. D-Ribulose 1,5-bisphosphate was first documented in 2004 (PMID: 15219406).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 29  0  0  0  0  0  0  0  0999 V2000
    1.5751   -0.7338    1.1738 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3092    0.0978    0.3123 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3533    1.0211   -0.2212 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3036    0.2391   -0.8573 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7007    0.1294    0.0984 P   0  0  1  0  0  5  0  0  0  0  0  0
    4.6195    1.2116    1.1600 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8096   -1.3435    0.8962 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0511    0.4357   -0.8748 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1063    0.1871   -0.1314 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2732    1.4460   -0.7049 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0728    0.0646    1.0152 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1383   -1.2492    1.4646 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4304    0.5239    0.5075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9294   -0.4386   -0.3533 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5615   -0.7621   -0.0585 P   0  0  2  0  0  5  0  0  0  0  0  0
   -4.7852   -0.6555    1.4381 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8827   -2.3334   -0.5606 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5180    0.3652   -0.8992 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8684    1.7537   -0.8847 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7592    1.5862    0.6436 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6917   -2.1256    0.3081 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7498   -0.2569   -0.7886 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3442   -0.5768   -0.9073 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0422    2.1182   -0.0071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7205    0.6868    1.8508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4847   -1.8216    0.7213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2592    1.4538   -0.0823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1582    0.6494    1.3221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0794   -2.8857   -0.3490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0050    1.2132   -0.8809 H   0  0  0  0  0  0  0  0  0  0  0  0
 12 11  1  0
 11 13  1  0
 13 14  1  0
 15 14  1  1
 15 17  1  0
 15 18  1  0
 15 16  2  0
 11  9  1  0
  9 10  1  0
  9  2  1  0
  2  1  2  0
  2  3  1  0
  3  4  1  0
  5  4  1  6
  5  7  1  0
  5  8  1  0
  5  6  2  0
 12 26  1  0
 11 25  1  1
 13 27  1  0
 13 28  1  0
 17 29  1  0
 18 30  1  0
  9 23  1  6
 10 24  1  0
  3 19  1  0
  3 20  1  0
  7 21  1  0
  8 22  1  0
M  END


  Mrv1652303062018502D          

 18 17  0  0  1  0            999 V2000
    7.1463  -18.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8597  -19.3497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5920  -18.9281    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.3055  -19.3423    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.0190  -18.9316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4328  -19.3462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8597  -20.1747    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5920  -18.1031    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3055  -20.1673    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0190  -18.1066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7085  -18.9133    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.3051  -19.6455    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9950  -18.4991    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1227  -18.1998    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7325  -17.6957    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   10.3217  -16.9823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.4460  -17.2850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1433  -18.4093    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  2  1  1  0  0  0  0
 11  6  1  0  0  0  0
  7  2  2  0  0  0  0
  3  2  1  0  0  0  0
  3  8  1  6  0  0  0
  4  3  1  0  0  0  0
  4  9  1  1  0  0  0
  5  4  1  0  0  0  0
 10  5  1  0  0  0  0
 15 10  1  0  0  0  0
 12 11  2  0  0  0  0
 13 11  1  0  0  0  0
 14 11  1  0  0  0  0
 16 15  2  0  0  0  0
 17 15  1  0  0  0  0
 18 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0054909

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3,5-6,8H,1-2H2,(H2,9,10,11)(H2,12,13,14)/t3-,5-/m1/s1

> <INCHI_KEY>
YAHZABJORDUQGO-NQXXGFSBSA-N

> <FORMULA>
C5H12O11P2

> <MOLECULAR_WEIGHT>
310.0897

> <EXACT_MASS>
309.98548425

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
22.437500389577625

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(3R,4R)-3,4-dihydroxy-2-oxo-5-(phosphonooxy)pentyl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-1.49

> <JCHEM_LOGP>
-2.8838290126666664

> <ALOGPS_LOGS>
-1.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.6549995885319904

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0021606343762866

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5803636984429508

> <JCHEM_POLAR_SURFACE_AREA>
191.04999999999995

> <JCHEM_REFRACTIVITY>
53.345099999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.21e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ribulose-1,5-bisphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-20         0                                  
HETATM    1  C   UNK     0      13.340 -35.346   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.671 -36.119   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.038 -35.332   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      17.370 -36.106   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      18.702 -35.339   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      12.008 -36.113   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      14.671 -37.659   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      16.038 -33.792   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      17.370 -37.646   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      18.702 -33.799   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0      10.656 -35.305   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0       9.903 -36.672   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       9.324 -34.532   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      11.429 -33.973   0.000  0.00  0.00           O+0
HETATM   15  P   UNK     0      20.034 -33.032   0.000  0.00  0.00           P+0
HETATM   16  O   UNK     0      19.267 -31.700   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      21.366 -32.265   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      20.801 -34.364   0.000  0.00  0.00           O+0
CONECT    1    6    2                                                       
CONECT    2    1    7    3                                                  
CONECT    3    2    8    4                                                  
CONECT    4    3    9    5                                                  
CONECT    5    4   10                                                       
CONECT    6    1   11                                                       
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5   15                                                       
CONECT   11    6   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
CONECT   15   10   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   15                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   34    0
END

View in JSmol

Synonyms

Value	Source
RIBULOSE-1,5-diphosphATE	ChEBI
RIBULOSE-1,5-diphosphoric acid	Generator
D-Ribulose 1,5-bisphosphoric acid	Generator
Ribulose-1,5-bisphosphate	MeSH
Ribulose-1,5 diphosphate	MeSH
Ribulose-1,5 diphosphate, (D)-isomer	MeSH
D-Ribulose-1,5-bisphosphoric acid	Generator

Chemical Formula

C₅H₁₂O₁₁P₂

Average Mass

310.0897 Da

Monoisotopic Mass

309.98548 Da

IUPAC Name

{[(3R,4R)-3,4-dihydroxy-2-oxo-5-(phosphonooxy)pentyl]oxy}phosphonic acid

Traditional Name

ribulose-1,5-bisphosphate

CAS Registry Number

Not Available

SMILES

O[C@H](COP(O)(O)=O)[C@@H](O)C(=O)COP(O)(O)=O

InChI Identifier

InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3,5-6,8H,1-2H2,(H2,9,10,11)(H2,12,13,14)/t3-,5-/m1/s1

InChI Key

YAHZABJORDUQGO-NQXXGFSBSA-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
Arabidopsis thaliana	Plant	KNApSAcK

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-5-phosphate
Pentose phosphate
Glycerone phosphate
Monosaccharide phosphate
Monoalkyl phosphate
Acyloin
Beta-hydroxy ketone
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Alpha-hydroxy ketone
Ketone
1,2-diol
Secondary alcohol
Carbonyl group
Hydrocarbon derivative
Alcohol
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ribulose phosphate (CHEBI:16710 )

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	-2.9	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	191.05 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	53.35 m³·mol⁻¹	ChemAxon
Polarizability	22.44 Å³	ChemAxon
Number of Rings	0	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB030796

KNApSAcK ID

C00007293

Chemspider ID

Not Available

KEGG Compound ID

C01182

BioCyc ID

D-RIBULOSE-15-P2

BiGG ID

Not Available

Wikipedia Link

Ribulose-1,5-bisphosphate

METLIN ID

Not Available

PubChem Compound

123658

PDB ID

Not Available

ChEBI ID

16710

Good Scents ID

Not Available

References

General References

Bhattacharya S, Schiavone M, Gomes J, Bhattacharya SK: Cascade of bioreactors in series for conversion of 3-phospho-D-glycerate into D-ribulose-1,5-bisphosphate: kinetic parameters of enzymes and operation variables. J Biotechnol. 2004 Jul 15;111(2):203-17. doi: 10.1016/j.jbiotec.2004.04.002. [PubMed:15219406 ]
Tcherkez GG, Bathellier C, Stuart-Williams H, Whitney S, Gout E, Bligny R, Badger M, Farquhar GD: D2O solvent isotope effects suggest uniform energy barriers in ribulose-1,5-bisphosphate carboxylase/oxygenase catalysis. Biochemistry. 2013 Feb 5;52(5):869-77. doi: 10.1021/bi300933u. Epub 2013 Jan 18. [PubMed:23301499 ]

Showing NP-Card for D-Ribulose 1,5-bisphosphate (NP0054909)

MOL for NP0054909 (D-Ribulose 1,5-bisphosphate)

3D MOL for NP0054909 (D-Ribulose 1,5-bisphosphate)

3D SDF for NP0054909 (D-Ribulose 1,5-bisphosphate)

3D-SDF for NP0054909 (D-Ribulose 1,5-bisphosphate)

PDB for NP0054909 (D-Ribulose 1,5-bisphosphate)

3D PDB for NP0054909 (D-Ribulose 1,5-bisphosphate)

SMILES for NP0054909 (D-Ribulose 1,5-bisphosphate)

INCHI for NP0054909 (D-Ribulose 1,5-bisphosphate)

Structure for NP0054909 (D-Ribulose 1,5-bisphosphate)

3D Structure for NP0054909 (D-Ribulose 1,5-bisphosphate)