MiMeDB: Showing metabocard for (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate (MMDBc0032125)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:03:24 UTC

Update Date

2022-08-31 18:30:43 UTC

Metabolite ID

MMDBc0032125

Metabolite Identification

Common Name

(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate

Description

(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate is a member of the chemical class known as Indoles. These are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole. (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate is involved in tryptophan biosynthesis. The latter is the competent substrate of (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate synthase, which catalyzes the subsequent step of tryptophan biosynthesis. (PMID 7727401 ) alphaTS by itself catalyzes the cleavage of indole-3-glycerol phosphate to glyceraldehyde-3-phosphate and indole, which is converted to tryptophan in tryptophan biosynthesis. (PMID 15879705 )

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 04091517012D          

 19 20  0  0  0  0            999 V2000
   -1.0607   -2.1035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5758   -1.4361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2087   -1.6910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9232   -1.2785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6377   -1.6910    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6377   -2.5160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9232   -2.9285    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2087   -2.5160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5758   -2.7709    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8307   -0.6514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2787   -0.0384    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5336    0.7462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0183    1.3593    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2365    2.1439    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4915    2.9285    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.5480    2.3988    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0211    1.8889    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.5282   -0.2099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6377   -0.4799    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  3  8  2  0  0  0  0
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
  2 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 14 17  1  0  0  0  0
 11 18  1  0  0  0  0
 10 19  1  0  0  0  0
M  CHG  2  15  -1  17  -1
M  END
> <DATABASE_ID>
MMDBc0032125

> <DATABASE_NAME>
MIME

> <SMILES>
OC(COP([O-])([O-])=O)C(O)C1=CNC2=C1C=CC=C2

> <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

> <INCHI_KEY>
NQEQTYPJSIEPHW-UHFFFAOYSA-L

> <FORMULA>
C11H12NO6P

> <MOLECULAR_WEIGHT>
285.193

> <EXACT_MASS>
285.041321268

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
25.523561762813166

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-(1H-indol-3-yl)-3-(phosphonatooxy)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>
6.512307194345704

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4864854788381807

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4498355399329927

> <JCHEM_POLAR_SURFACE_AREA>
128.67000000000002

> <JCHEM_REFRACTIVITY>
64.51490000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-(1H-indol-3-yl)-3-(phosphonatooxy)propane-1,2-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-APR-15         0                                  
HETATM    1  C   UNK     0      -1.980  -3.927   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.075  -2.681   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.390  -3.157   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.723  -2.387   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.057  -3.157   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.057  -4.697   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.723  -5.467   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.390  -4.697   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -1.075  -5.172   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      -1.551  -1.216   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.520  -0.072   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.996   1.393   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.034   2.537   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0      -0.441   4.002   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0      -0.917   5.467   0.000  0.00  0.00           O-1
HETATM   16  O   UNK     0       1.023   4.478   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.906   3.526   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0       0.986  -0.392   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -3.057  -0.896   0.000  0.00  0.00           O+0
CONECT    1    2    9                                                       
CONECT    2    1    3   10                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3    9                                                  
CONECT    9    8    1                                                       
CONECT   10    2   11   19                                                  
CONECT   11   10   12   18                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14                                                            
CONECT   18   11                                                            
CONECT   19   10                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

Synonyms

Value	Source
1-C-(indol-3-yl)Glycerol 3-phosphate (2-)	ChEBI
1-C-(indol-3-yl)Glycerol 3-phosphate dianion	ChEBI
1-C-(indol-3-yl)Glycerol 3-phosphoric acid (2-)	Generator
1-C-(indol-3-yl)Glycerol 3-phosphoric acid dianion	Generator
(1S,2R)-1-C-(indol-3-yl)Glycerol 3-phosphoric acid	Generator

Molecular Formula

C₁₁H₁₂NO₆P

Average Mass

285.193

Monoisotopic Mass

285.041321268

IUPAC Name

1-(1H-indol-3-yl)-3-(phosphonatooxy)propane-1,2-diol

Traditional Name

1-(1H-indol-3-yl)-3-(phosphonatooxy)propane-1,2-diol

CAS Registry Number

Not Available

SMILES

OC(COP([O-])([O-])=O)C(O)C1=CNC2=C1C=CC=C2

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

InChI Key

NQEQTYPJSIEPHW-UHFFFAOYSA-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:60820 )
an indole-containing compound (INDOLE-3-GLYCEROL-P )

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	25.52 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-d6edd9533591edccc5fe	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001r-0190000000-33fd31bb35f5c119d546	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01qa-6910000000-1c2758a367c37aff8144	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0090000000-29f156f93694c4e1ed43	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-2190000000-dc2560f39d55366ecadb	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003s-9100000000-03955eeb8f28e1b25ab3	2015-09-15	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0014340	1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate	(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate	Indole-3-glycerol phosphate synthase	Synthesis	RHEA	34755880
MMDBr0017834	(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate	D-Glyceraldehyde 3-phosphate	Tryptophan synthase	Synthesis	RHEA	34755880
MMDBr0018282	Hydrogen Ion	Carbon dioxide	Tryptophan biosynthesis protein TrpCF	Synthesis	PathBank	31602464
MMDBr0018283	(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate	Indole	Tryptophan synthase alpha chain	Synthesis	PathBank	31602464
MMDBr0018945	Hydrogen Ion	Carbon dioxide	Tryptophan biosynthesis protein TrpCF	Synthesis	PathBank	31602464

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
Bacteria	Proteobacteria	380	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Turkey ; Sheep ; Pig ; Chicken ; Cattle ; River trout ; Human subgingival plaque	Unknown
Bacteria	Cyanobacteria	32	Human
Bacteria	Firmicutes	103	Human feces; Human ; Human supragingival plaque; Catfish ; Cattle
Archaea/Archaea	Crenarchaeota	9
Bacteria	Aquificae	2
Bacteria	Actinobacteria	49	Human feces; Human ; Cattle
Bacteria/NULL	Proteobacteria	3	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Turkey ; Sheep ; Pig ; Chicken ; Cattle ; River trout ; Human subgingival plaque	Unknown
Bacteria	Bacteroidetes	11	Human ; Human feces
Bacteria	Chlorobi	11
Bacteria	Chloroflexi	9
Bacteria	Deinococcus-thermus	3
Bacteria	Elusimicrobia	2
Archaea/Archaea	Euryarchaeota	30
Bacteria	Acidobacteria	2
Bacteria	Spirochaetes	6	Human
Bacteria	Verrucomicrobia	1
Bacteria	Thermotogae	8
Bacteria	Planctomycetes	1
Archaea	Crenarchaeota	1
Bacteria	nah	1
Eukaryota/Fungi	Ascomycota	10	Human feces; Human saliva	Unknown
Eukaryota/Fungi	Basidiomycota	6	Human feces
Eukaryota/Fungi	Mucoromycota	1	Human feces
Bacteria	Chlamydiae	3	Cat ; Human
Bacteria	Dictyoglomi	2
Archaea	Euryarchaeota	1
Bacteria	Fusobacteria	1	Human ; Human feces

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

25246146

PDB ID

Not Available

ChEBI ID

60820

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate (MMDBc0032125)

MOL for #<Metabolite:0x00007f5abc4e97b0>

3D MOL for #<Metabolite:0x00007f5abc4e97b0>

3D SDF for #<Metabolite:0x00007f5abc4e97b0>

3D-SDF for #<Metabolite:0x00007f5abc4e97b0>

PDB for #<Metabolite:0x00007f5abc4e97b0>

3D PDB for #<Metabolite:0x00007f5abc4e97b0>

SMILES for #<Metabolite:0x00007f5abc4e97b0>

INCHI for #<Metabolite:0x00007f5abc4e97b0>

Structure for #<Metabolite:0x00007f5abc4e97b0>

3D Structure for #<Metabolite:0x00007f5abc4e97b0>