Np mrd loader

Showing NP-Card for Indoxyl (NP0000891)

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Record Information
Version1.0
Created at2006-08-13 10:46:17 UTC
Updated at2021-06-29 00:47:52 UTC
NP-MRD IDNP0000891
Secondary Accession NumbersNone
Natural Product Identification
Common NameIndoxyl
DescriptionIndoxyl, also known as 1H-indol-3-ol, belongs to the class of organic compounds known as hydroxyindoles. These are organic compounds containing an indole moiety that carries a hydroxyl group. Indoxyl is isomeric with oxindol and is obtained as an oily liquid. Indoxyl exists in all living organisms, ranging from bacteria to humans. Indoxyl is obtained from indican, which is a glycoside. Obermayer's reagent is a dilute solution FeCl3 in hydrochloric acid. The hydrolysis of indican yields β-D-glucose and indoxyl. Indigo dye is a product of the reaction of indoxyl by a mild oxidizing agent such as atmospheric oxygen. In chemistry, indoxyl is a nitrogenous substance with the chemical formula: C8H7NO. Indoxyl can be found in urine and is titrated with Obermayer's reagent.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000891 (Indoxyl)


  Mrv1652305271900162D          

 10 11  0  0  0  0            999 V2000
   24.1110  -12.4368    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.8548  -14.5489    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.8548  -13.2210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0742  -14.2974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0742  -13.4724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.3363  -13.8849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.3596  -14.7099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.3596  -13.0599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.6451  -14.2974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.6451  -13.4724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  6  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  2  0  0  0  0
  4  5  1  0  0  0  0
  4  7  2  0  0  0  0
  5  8  2  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 10  2  0  0  0  0
M  END
Download

3D MOL for NP0000891 (Indoxyl)

HMDB0004094
     RDKit          3D
Indoxyl
 17 18  0  0  0  0  0  0  0  0999 V2000
    2.9861   -0.0262   -0.0708 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6995   -0.5431   -0.1282 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3838   -1.8667   -0.3413 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0427   -1.9483   -0.3250 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5185   -0.7519   -0.1135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8255   -0.2904   -0.0077 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1280    1.0327    0.2192 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0947    1.9231    0.3443 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2136    1.4951    0.2440 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5215    0.1602    0.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1148    0.9676    0.0916 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0826   -2.7041   -0.4962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4693   -2.8481   -0.4633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6024   -1.0570   -0.1179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1644    1.3270    0.2912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2911    2.9576    0.5207 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0492    2.1726    0.3380 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  2  1  0
 10  5  1  0
  1 11  1  0
  3 12  1  0
  4 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
M  END
Download

3D SDF for NP0000891 (Indoxyl)


  Mrv1652305271900162D          

 10 11  0  0  0  0            999 V2000
   24.1110  -12.4368    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.8548  -14.5489    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.8548  -13.2210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0742  -14.2974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0742  -13.4724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.3363  -13.8849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.3596  -14.7099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.3596  -13.0599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.6451  -14.2974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.6451  -13.4724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  6  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  2  0  0  0  0
  4  5  1  0  0  0  0
  4  7  2  0  0  0  0
  5  8  2  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 10  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0000891

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CNC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C8H7NO/c10-8-5-9-7-4-2-1-3-6(7)8/h1-5,9-10H

> <INCHI_KEY>
PCKPVGOLPKLUHR-UHFFFAOYSA-N

> <FORMULA>
C8H7NO

> <MOLECULAR_WEIGHT>
133.1473

> <EXACT_MASS>
133.052763851

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
13.780140299547636

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1H-indol-3-ol

> <ALOGPS_LOGP>
1.29

> <JCHEM_LOGP>
1.768442487333333

> <ALOGPS_LOGS>
-1.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.369886121128292

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.148720316813929

> <JCHEM_PKA_STRONGEST_BASIC>
-6.265104403410967

> <JCHEM_POLAR_SURFACE_AREA>
36.019999999999996

> <JCHEM_REFRACTIVITY>
39.1254

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.67e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
indoxyl

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0000891 (Indoxyl)

HMDB0004094
     RDKit          3D
Indoxyl
 17 18  0  0  0  0  0  0  0  0999 V2000
    2.9861   -0.0262   -0.0708 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6995   -0.5431   -0.1282 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3838   -1.8667   -0.3413 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0427   -1.9483   -0.3250 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5185   -0.7519   -0.1135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8255   -0.2904   -0.0077 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1280    1.0327    0.2192 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0947    1.9231    0.3443 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2136    1.4951    0.2440 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5215    0.1602    0.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1148    0.9676    0.0916 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0826   -2.7041   -0.4962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4693   -2.8481   -0.4633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6024   -1.0570   -0.1179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1644    1.3270    0.2912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2911    2.9576    0.5207 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0492    2.1726    0.3380 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  2  1  0
 10  5  1  0
  1 11  1  0
  3 12  1  0
  4 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
M  END
Download

PDB for NP0000891 (Indoxyl)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      45.007 -23.215   0.000  0.00  0.00           O+0
HETATM    2  N   UNK     0      44.529 -27.158   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      44.529 -24.679   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      43.072 -26.688   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      43.072 -25.148   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      45.428 -25.918   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      41.738 -27.458   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      41.738 -24.378   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      40.404 -26.688   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      40.404 -25.148   0.000  0.00  0.00           C+0
CONECT    1    3                                                            
CONECT    2    4    6                                                       
CONECT    3    1    5    6                                                  
CONECT    4    2    5    7                                                  
CONECT    5    3    4    8                                                  
CONECT    6    2    3                                                       
CONECT    7    4    9                                                       
CONECT    8    5   10                                                       
CONECT    9    7   10                                                       
CONECT   10    8    9                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END
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3D PDB for NP0000891 (Indoxyl)

COMPND    HMDB0004094
HETATM    1  O1  UNL     1       2.986  -0.026  -0.071  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.699  -0.543  -0.128  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.384  -1.867  -0.341  1.00  0.00           C  
HETATM    4  N1  UNL     1       0.043  -1.948  -0.325  1.00  0.00           N  
HETATM    5  C3  UNL     1      -0.518  -0.752  -0.114  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.826  -0.290  -0.008  1.00  0.00           C  
HETATM    7  C5  UNL     1      -2.128   1.033   0.219  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.095   1.923   0.344  1.00  0.00           C  
HETATM    9  C7  UNL     1       0.214   1.495   0.244  1.00  0.00           C  
HETATM   10  C8  UNL     1       0.522   0.160   0.015  1.00  0.00           C  
HETATM   11  H1  UNL     1       3.115   0.968   0.092  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.083  -2.704  -0.496  1.00  0.00           H  
HETATM   13  H3  UNL     1      -0.469  -2.848  -0.463  1.00  0.00           H  
HETATM   14  H4  UNL     1      -2.602  -1.057  -0.118  1.00  0.00           H  
HETATM   15  H5  UNL     1      -3.164   1.327   0.291  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.291   2.958   0.521  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.049   2.173   0.338  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3    3   10
CONECT    3    4   12
CONECT    4    5   13
CONECT    5    6    6   10
CONECT    6    7   14
CONECT    7    8    8   15
CONECT    8    9   16
CONECT    9   10   10   17
END
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SMILES for NP0000891 (Indoxyl)

OC1=CNC2=CC=CC=C12
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INCHI for NP0000891 (Indoxyl)

InChI=1S/C8H7NO/c10-8-5-9-7-4-2-1-3-6(7)8/h1-5,9-10H
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View in JSmol
Synonyms
ValueSource
1H-indol-3-OlChEBI
Chemical FormulaC8H7NO
Average Mass133.1473 Da
Monoisotopic Mass133.05276 Da
IUPAC Name1H-indol-3-ol
Traditional Nameindoxyl
CAS Registry Number480-93-3
SMILES
OC1=CNC2=CC=CC=C12
InChI Identifier
InChI=1S/C8H7NO/c10-8-5-9-7-4-2-1-3-6(7)8/h1-5,9-10H
InChI KeyPCKPVGOLPKLUHR-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)Varshavi.d262021-09-05View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Varshavi.d262021-09-05View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)V.dorna832021-08-03View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Haliclona oculataLOTUS Database
Isatis tinctoriaLOTUS Database
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Uncaria elliptica R.Br.ex G.Don.KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxyindoles. These are organic compounds containing an indole moiety that carries a hydroxyl group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIndoles and derivatives
Sub ClassHydroxyindoles
Direct ParentHydroxyindoles
Alternative Parents
Substituents
  • Hydroxyindole
  • Indole
  • Benzenoid
  • Substituted pyrrole
  • Heteroaromatic compound
  • Pyrrole
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility7.67 g/LALOGPS
logP1.29ALOGPS
logP1.77ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)9.15ChemAxon
pKa (Strongest Basic)-6.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area36.02 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity39.13 m³·mol⁻¹ChemAxon
Polarizability13.78 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0004094
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023310
KNApSAcK IDC00025147
Chemspider ID45861
KEGG Compound IDC05658
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkIndoxyl
METLIN ID7014
PubChem Compound50591
PDB IDNot Available
ChEBI ID17840
Good Scents IDNot Available
References
General References
  1. Achtergael W, Michielsen D, Gorus FK, Gerlo E: Indoxyl sulphate and the purple urine bag syndrome: a case report. Acta Clin Belg. 2006 Jan-Feb;61(1):38-41. [PubMed:16673616 ]
  2. Delisle GJ, Ley A: Rapid detection of Escherichia coli in urine samples by a new chromogenic beta-glucuronidase assay. J Clin Microbiol. 1989 Apr;27(4):778-9. [PubMed:2656750 ]
  3. Nazzal L, Soiefer L, Chang M, Tamizuddin F, Schatoff D, Cofer L, Aguero-Rosenfeld ME, Matalon A, Meijers B, Holzman R, Lowenstein J: Effect of Vancomycin on the Gut Microbiome and Plasma Concentrations of Gut-Derived Uremic Solutes. Kidney Int Rep. 2021 May 19;6(8):2122-2133. doi: 10.1016/j.ekir.2021.05.014. eCollection 2021 Aug. [PubMed:34386661 ]
  4. Hsieh YH, Hung TW, Chen YS, Huang YN, Chiou HL, Lee CC, Tsai JP: In Vitro and In Vivo Antifibrotic Effects of Fraxetin on Renal Interstitial Fibrosis via the ERK Signaling Pathway. Toxins (Basel). 2021 Jul 9;13(7). pii: toxins13070474. doi: 10.3390/toxins13070474. [PubMed:34357946 ]
  5. Margiotta E, Caldiroli L, Callegari ML, Miragoli F, Zanoni F, Armelloni S, Rizzo V, Messa P, Vettoretti S: Association of Sarcopenia and Gut Microbiota Composition in Older Patients with Advanced Chronic Kidney Disease, Investigation of the Interactions with Uremic Toxins, Inflammation and Oxidative Stress. Toxins (Basel). 2021 Jul 8;13(7). pii: toxins13070472. doi: 10.3390/toxins13070472. [PubMed:34357944 ]
  6. Ichimura Y, Kudoh N, Murabe T, Akao T, Watanuki S, Suzuki T, Saito T, Oda M, Saitoh H: Inhibitory effects of indoxyl sulfate and creatinine on the renal transport of meropenem and biapenem in rats. Drug Metab Pharmacokinet. 2021 May 31;40:100406. doi: 10.1016/j.dmpk.2021.100406. [PubMed:34352708 ]
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  8. Savira F, Magaye R, Scullino CV, Flynn BL, Pitson SM, Anderson D, Creek DJ, Hua Y, Xiong X, Huang L, Liew D, Reid C, Kaye D, Kompa AR, Wang BH: Sphingolipid imbalance and inflammatory effects induced by uremic toxins in heart and kidney cells are reversed by dihydroceramide desaturase 1 inhibition. Toxicol Lett. 2021 Jul 22;350:133-142. doi: 10.1016/j.toxlet.2021.07.012. [PubMed:34303789 ]
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