MiMeDB: Showing metabocard for 1-C-(3-indolyl)-glycerol 3-phosphate (MMDBc0047848)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 15:45:48 UTC

Update Date

2022-09-01 02:00:00 UTC

Metabolite ID

MMDBc0047848

Metabolite Identification

Common Name

1-C-(3-indolyl)-glycerol 3-phosphate

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303082008132D          

 21 22  0  0  0  0            999 V2000
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -0.8853    0.0000 C   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
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752    0.5124    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358   -0.5422    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4950   -2.6260    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.0247   -1.5865    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.4554   -2.0964    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851   -1.0568    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400   -1.8414    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.6288   -0.7137    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3317    0.6840    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  7  3  2  0  0  0  0
  8  5  2  0  0  0  0
  8  7  1  0  0  0  0
  9  4  2  0  0  0  0
  9  7  1  0  0  0  0
 10  6  1  0  0  0  0
 11  8  1  0  0  0  0
 11 10  1  0  0  0  0
 12  5  1  0  0  0  0
 12  9  1  0  0  0  0
 10 13  1  6  0  0  0
 11 14  1  1  0  0  0
 18  6  1  0  0  0  0
 19 15  1  0  0  0  0
 19 16  1  0  0  0  0
 19 17  2  0  0  0  0
 19 18  1  0  0  0  0
 10 20  1  6  0  0  0
 11 21  1  1  0  0  0
M  CHG  2  15  -1  16  -1
M  END
> <DATABASE_ID>
MMDBc0047848

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(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)/p-2/t10-,11+/m1/s1

> <INCHI_KEY>
NQEQTYPJSIEPHW-MNOVXSKESA-L

> <FORMULA>
C11H12NO6P

> <MOLECULAR_WEIGHT>
285.1898

> <EXACT_MASS>
285.040223633

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
25.602029285959254

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2R)-1-(1H-indol-3-yl)-3-(phosphonooxy)propane-1,2-diol

> <ALOGPS_LOGP>
0.12

> <JCHEM_LOGP>
-0.07957787366666655

> <ALOGPS_LOGS>
-1.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.512307194345705

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4864854788381807

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4498355399329927

> <JCHEM_POLAR_SURFACE_AREA>
128.67

> <JCHEM_REFRACTIVITY>
64.5149

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R)-1-(1H-indol-3-yl)-3-(phosphonooxy)propane-1,2-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.332  -1.653   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.143  -0.188   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0      -0.887   0.956   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       2.680  -1.012   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -2.791  -4.902   0.000  0.00  0.00           O-1
HETATM   16  O   UNK     0      -3.779  -2.961   0.000  0.00  0.00           O-1
HETATM   17  O   UNK     0      -0.850  -3.913   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -1.839  -1.973   0.000  0.00  0.00           O+0
HETATM   19  P   UNK     0      -2.315  -3.437   0.000  0.00  0.00           P+0
HETATM   20  H   UNK     0       1.174  -1.332   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.619   1.277   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    7                                                       
CONECT    4    2    9                                                       
CONECT    5    8   12                                                       
CONECT    6   10   18                                                       
CONECT    7    3    8    9                                                  
CONECT    8    5    7   11                                                  
CONECT    9    4    7   12                                                  
CONECT   10    6   11   13   20                                             
CONECT   11    8   10   14   21                                             
CONECT   12    5    9                                                       
CONECT   13   10                                                            
CONECT   14   11                                                            
CONECT   15   19                                                            
CONECT   16   19                                                            
CONECT   17   19                                                            
CONECT   18    6   19                                                       
CONECT   19   15   16   17   18                                             
CONECT   20   10                                                            
CONECT   21   11                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

Synonyms

Value	Source
(1S,2R)-1-(1H-indol-3-yl)-3-(Phosphonatooxy)propane-1,2-diol	ChEBI
(1S,2R)-1-C-(indol-3-yl)Glycerol 3-phosphate	ChEBI
(1S,2R)-1-C-(indol-3-yl)Glycerol 3-phosphoric acid	Generator
Indoleglycerol phosphoric acid	Generator
(1S,2R)-1-C-(indol-3-yl)Glycerol 3-phosphoric acid(2-)	Generator
Indole-3-glycerol phosphate	MeSH
Indole-3-glycerophosphate	MeSH
Indoleglycerol phosphate	MeSH

Molecular Formula

C₁₁H₁₂NO₆P

Average Mass

285.1898

Monoisotopic Mass

285.040223633

IUPAC Name

(1S,2R)-1-(1H-indol-3-yl)-3-(phosphonooxy)propane-1,2-diol

Traditional Name

(1S,2R)-1-(1H-indol-3-yl)-3-(phosphonooxy)propane-1,2-diol

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(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)/p-2/t10-,11+/m1/s1

InChI Key

NQEQTYPJSIEPHW-MNOVXSKESA-L

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
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
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:58866 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	20.5 g/L	ALOGPS
logP	0.12	ALOGPS
logP	-0.08	ChemAxon
logS	-1.2	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	3	ChemAxon
Polar Surface Area	128.67 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	64.51 m³·mol⁻¹	ChemAxon
Polarizability	25.6 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0090000000-156bbda0afbe645d16fa	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001r-0190000000-decb1dc59950a615af5a	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01qa-6910000000-b40fb2b4a925ffa6951f	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0090000000-e171a0b1f22533d00ce0	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-2190000000-f448ea08e17f0bd7f8e4	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003s-9100000000-e68bf1f5d04521ec9a35	2016-09-14	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB 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

46878464

PDB ID

Not Available

ChEBI ID

58866

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Ramirez-Gaona M, Marcu A, Pon A, Guo AC, Sajed T, Wishart NA, Karu N, Djoumbou Feunang Y, Arndt D, Wishart DS: YMDB 2.0: a significantly expanded version of the yeast metabolome database. Nucleic Acids Res. 2017 Jan 4;45(D1):D440-D445. doi: 10.1093/nar/gkw1058. Epub 2016 Nov 28. [PubMed:27899612 ]

Showing metabocard for 1-C-(3-indolyl)-glycerol 3-phosphate (MMDBc0047848)

MOL for #<Metabolite:0x00007fecfea064f8>

3D MOL for #<Metabolite:0x00007fecfea064f8>

3D SDF for #<Metabolite:0x00007fecfea064f8>

3D-SDF for #<Metabolite:0x00007fecfea064f8>

PDB for #<Metabolite:0x00007fecfea064f8>

3D PDB for #<Metabolite:0x00007fecfea064f8>

SMILES for #<Metabolite:0x00007fecfea064f8>

INCHI for #<Metabolite:0x00007fecfea064f8>

Structure for #<Metabolite:0x00007fecfea064f8>

3D Structure for #<Metabolite:0x00007fecfea064f8>