NP-MRD: Showing NP-Card for Indole-3-glycerol phosphate (NP0054893)

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Record Information

Version

2.0

Created at

2022-04-28 01:05:57 UTC

Updated at

2022-04-28 01:05:57 UTC

NP-MRD ID

NP0054893

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Indole-3-glycerol phosphate

Description

[(2S,3R)-2,3-dihydroxy-3-(1H-indol-3-yl)propoxy]phosphonic acid belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position. Indole-3-glycerol phosphate is found in Arabidopsis thaliana and Escherichia coli. Based on a literature review very few articles have been published on [(2S,3R)-2,3-dihydroxy-3-(1H-indol-3-yl)propoxy]phosphonic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 34  0  0  0  0  0  0  0  0999 V2000
   -4.2668   -1.6457    0.6388 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3555   -0.3224   -0.1035 P   0  0  2  0  0  5  0  0  0  0  0  0
   -4.3843    0.9389    1.1611 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7653   -0.1633   -0.9251 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9358   -0.0175   -0.8552 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1052   -1.1362   -0.8937 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7969   -0.6811   -0.2270 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0706   -0.5504    1.1543 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2827    0.6756   -0.7568 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0865    0.7213   -2.0582 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9588    0.8283    0.0958 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1175    1.4545    1.2836 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3511    1.2226    1.7065 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0022    0.4470    0.7703 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2040   -0.1321    0.6619 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5286   -0.8902   -0.3709 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6608   -1.1572   -1.4218 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4269   -0.5967   -1.3404 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0796    0.2184   -0.2407 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1433    1.7403    0.5687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2452    0.7090   -0.6982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7807   -1.2957   -1.9771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4708   -2.0363   -0.5231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0072   -1.3929   -0.3885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2296    0.3624    1.4320 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0353    1.4752   -0.3984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5934    1.4192   -2.5698 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3324    2.0383    1.8316 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7450    1.5522    2.6191 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9367    0.0308    1.4694 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5449   -1.3323   -0.4092 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9402   -1.7391   -2.2850 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7267   -0.7450   -2.1325 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  2  5  1  6
  2  3  1  0
  2  4  1  0
  2  1  2  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 11  1  0
 19 14  1  0
  8 25  1  0
  7 24  1  1
  6 22  1  0
  6 23  1  0
  3 20  1  0
  4 21  1  0
  9 26  1  1
 10 27  1  0
 12 28  1  0
 13 29  1  0
 15 30  1  0
 16 31  1  0
 17 32  1  0
 18 33  1  0
M  END


  Mrv1652304282203052D          

 19 20  0  0  1  0            999 V2000
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -2.1500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2054   -2.3215    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4604   -3.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2673   -3.2777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5223   -4.0623    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7772   -4.8469    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7376   -4.3172    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3069   -3.8074    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7575   -1.7084    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1536   -2.7631    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 C   0  0  0  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  1  0  0  0  0
  4  5  2  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 10 13  1  0  0  0  0
  7 14  1  6  0  0  0
  6 15  1  1  0  0  0
  2 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
  1 19  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0054893

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H](COP(O)(O)=O)[C@H](O)C1=CNC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C11H14NO6P/c13-10(6-18-19(15,16)17)11(14)8-5-12-9-4-2-1-3-7(8)9/h1-5,10-14H,6H2,(H2,15,16,17)/t10-,11+/m0/s1

> <INCHI_KEY>
NQEQTYPJSIEPHW-WDEREUQCSA-N

> <FORMULA>
C11H14NO6P

> <MOLECULAR_WEIGHT>
287.208

> <EXACT_MASS>
287.055874173

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
26.166398462639314

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[(2S,3R)-2,3-dihydroxy-3-(1H-indol-3-yl)propoxy]phosphonic acid

> <ALOGPS_LOGP>
-0.21

> <JCHEM_LOGP>
-0.07957787366666655

> <ALOGPS_LOGS>
-1.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.512307194345704

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4864854788381807

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4498355399329927

> <JCHEM_POLAR_SURFACE_AREA>
123.01000000000002

> <JCHEM_REFRACTIVITY>
66.7583

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.87e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R)-2,3-dihydroxy-3-(1H-indol-3-yl)propoxyphosphonic 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       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.268  -2.549   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.744  -4.013   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.250  -4.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.726  -5.798   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -4.232  -6.118   0.000  0.00  0.00           O+0
HETATM   10  P   UNK     0      -4.708  -7.583   0.000  0.00  0.00           P+0
HETATM   11  O   UNK     0      -5.184  -9.048   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -3.244  -8.059   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -6.173  -7.107   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -3.281  -3.189   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.287  -5.158   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       2.530   0.237   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.864  -0.533   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.864  -2.073   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.530  -2.843   0.000  0.00  0.00           C+0
CONECT    1    2    5   19                                                  
CONECT    2    1    3   16                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1    6                                                  
CONECT    6    5    7   15                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12   13                                             
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13   10                                                            
CONECT   14    7                                                            
CONECT   15    6                                                            
CONECT   16    2   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18    1                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

View in JSmol

Synonyms

Value	Source
[(2S,3R)-2,3-Dihydroxy-3-(1H-indol-3-yl)propoxy]phosphonate	Generator

Chemical Formula

C₁₁H₁₄NO₆P

Average Mass

287.2080 Da

Monoisotopic Mass

287.05587 Da

IUPAC Name

[(2S,3R)-2,3-dihydroxy-3-(1H-indol-3-yl)propoxy]phosphonic acid

Traditional Name

(2S,3R)-2,3-dihydroxy-3-(1H-indol-3-yl)propoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

O[C@@H](COP(O)(O)=O)[C@H](O)C1=CNC2=CC=CC=C12

InChI Identifier

InChI=1S/C11H14NO6P/c13-10(6-18-19(15,16)17)11(14)8-5-12-9-4-2-1-3-7(8)9/h1-5,10-14H,6H2,(H2,15,16,17)/t10-,11+/m0/s1

InChI Key

NQEQTYPJSIEPHW-WDEREUQCSA-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
Escherichia coli	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

3-alkylindoles

Alternative Parents

Substituents

3-alkylindole
Monoalkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Substituted pyrrole
Alkyl phosphate
Benzenoid
Pyrrole
Heteroaromatic compound
Secondary alcohol
1,2-diol
Azacycle
Hydrocarbon derivative
Organic oxide
Aromatic alcohol
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Alcohol
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	-0.21	ALOGPS
logP	-0.08	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.49	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	123.01 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	66.76 m³·mol⁻¹	ChemAxon
Polarizability	26.17 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

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

138454307

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Indole-3-glycerol phosphate (NP0054893)

MOL for NP0054893 (Indole-3-glycerol phosphate)

3D MOL for NP0054893 (Indole-3-glycerol phosphate)

3D SDF for NP0054893 (Indole-3-glycerol phosphate)

3D-SDF for NP0054893 (Indole-3-glycerol phosphate)

PDB for NP0054893 (Indole-3-glycerol phosphate)

3D PDB for NP0054893 (Indole-3-glycerol phosphate)

SMILES for NP0054893 (Indole-3-glycerol phosphate)

INCHI for NP0054893 (Indole-3-glycerol phosphate)

Structure for NP0054893 (Indole-3-glycerol phosphate)

3D Structure for NP0054893 (Indole-3-glycerol phosphate)