Hmdb loader

Showing metabocard for Rhodamine B (HMDB0031786)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:45:27 UTC
Update Date2022-03-07 02:53:07 UTC
HMDB IDHMDB0031786
Secondary Accession Numbers
  • HMDB31786
Metabolite Identification
Common NameRhodamine B
DescriptionRhodamine B (RhB), also known as rhodamine 610 chloride (CAS: 81-88-9), belongs to the class of organic compounds known as xanthenes. These are polycyclic aromatic compounds containing a xanthene moiety, which consists of two benzene rings joined to each other by a pyran ring. Rhodamine B is a highly-soluble, basic, red, synthetic dye that is widely used in many industries (e.g. paper, plastic, textiles, ceramics, cosmetics). In the past, it was used extensively as a low-cost food colourant (e.g. in paprika- and chilli-containing foods) but it has since been prohibited for use as a food additive due to its carcinogenicity, reproductive and developmental toxicity, and neurotoxicity (PMID: 30463493 ). Due to its photostability and solubility, rhodamine B is also used as a fluorescent dye to stain biological tissues (PMID: 28957318 ).
Structure
Data?1593026659
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031786 (Rhodamine B)


  Mrv1652306242021232D          

 33 36  0  0  0  0            999 V2000
10001.4291 9998.7788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.1427 9998.3647    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.4291 9999.6028    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.149910001.6370    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10002.858310001.6370    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9996.435110001.2260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.149910002.4610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.573910001.2260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.858310002.4610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.722410001.6370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.435110002.8740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.287510001.6370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.573910002.8740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0023 9997.1284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7167 9997.5409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7167 9998.3660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0023 9998.7785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2878 9998.3660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2878 9997.5409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.4311 9999.9888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.145710000.4014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.145710001.2263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.431210001.6389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0033 9999.9887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.717810000.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.717810001.2263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.003310001.6387    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
 9997.861110000.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5756 9999.9888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.290110000.4013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.290210001.2263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.575710001.6388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.861110001.2262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  4  6  1  0  0  0  0
  4  7  1  0  0  0  0
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  5  9  1  0  0  0  0
  6 10  1  0  0  0  0
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 33  4  1  0  0  0  0
 27 31  2  0  0  0  0
 24 30  2  0  0  0  0
M  CHG  1  27   1
M  END
Download

3D MOL for HMDB0031786 (Rhodamine B)

HMDB0031786
     RDKit          3D
Rhodamine B
 64 67  0  0  0  0  0  0  0  0999 V2000
   -5.2281    3.1879   -0.9780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1693    1.7000   -1.2842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9004    0.9110   -0.1119 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7970    0.7437    0.9850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0115    1.9771    1.8160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6218    0.2385   -0.0689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5144   -1.1170   -0.1743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2584   -1.7072   -0.1574 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1338   -0.9294   -0.0355 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1247   -1.5311   -0.0221 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2744   -2.9694   -0.1072 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2476   -3.7593    1.0511 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3494   -5.1255    1.0106 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4823   -5.7062   -0.2216 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5170   -4.9808   -1.4177 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4112   -3.6087   -1.3340 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4494   -2.8187   -2.5646 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5781   -3.4664   -3.6666 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3589   -1.4582   -2.6394 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2058   -0.7036    0.0970 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4829   -1.1734    0.1151 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5549   -0.3185    0.2299 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3739    1.0435    0.3309 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4704    1.9369    0.4287 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2001    2.0232    1.6655 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6672    1.0279    2.6492 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    2.7510   -0.7165 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1157    2.3582   -1.3362 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0786    1.5344    0.3142 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0026    0.6793    0.1983 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1799    1.2128    0.1853 O   0  0  0  0  0  3  0  0  0  0  0  0
   -1.2542    0.4374    0.0699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5036    1.0162    0.0537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3091    3.5814   -0.5437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1561    3.4340   -0.4195 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3549    3.7005   -1.9754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0901    1.4036   -1.7789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3572    1.6015   -2.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4388   -0.0600    1.6603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7559    0.3581    0.5558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0032    2.4415    1.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1646    2.6920    1.7425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0370    1.7174    2.9203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3943   -1.7110   -0.2726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1094   -2.7738   -0.2345 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1417   -3.2615    2.0009 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3254   -5.7322    1.9264 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5629   -6.7883   -0.3053 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6244   -5.4999   -2.3831 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5289   -0.9733   -3.5043 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6291   -2.2588    0.0348 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5600   -0.7502    0.2333 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0657    3.0581    2.1268 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3001    1.9634    1.5086 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9627    1.3071    3.7035 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1427    0.0329    2.4083 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5778    0.9445    2.5333 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9890    2.7091   -1.4587 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9146    3.8433   -0.3856 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6003    1.5806   -0.7476 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9402    2.0468   -2.3984 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7644    3.2665   -1.4119 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9048    2.6172    0.3931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5469    2.1039    0.1385 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  3  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 17 19  1  0
 10 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 24 27  1  0
 27 28  1  0
 23 29  2  0
 29 30  1  0
 30 31  2  0
 31 32  1  0
 32 33  2  0
 33  6  1  0
 32  9  1  0
 16 11  1  0
 30 20  1  0
  1 34  1  0
  1 35  1  0
  1 36  1  0
  2 37  1  0
  2 38  1  0
  4 39  1  0
  4 40  1  0
  5 41  1  0
  5 42  1  0
  5 43  1  0
  7 44  1  0
  8 45  1  0
 12 46  1  0
 13 47  1  0
 14 48  1  0
 15 49  1  0
 19 50  1  0
 21 51  1  0
 22 52  1  0
 25 53  1  0
 25 54  1  0
 26 55  1  0
 26 56  1  0
 26 57  1  0
 27 58  1  0
 27 59  1  0
 28 60  1  0
 28 61  1  0
 28 62  1  0
 29 63  1  0
 33 64  1  0
M  CHG  1  31   1
M  END
Download

3D SDF for HMDB0031786 (Rhodamine B)


  Mrv1652306242021232D          

 33 36  0  0  0  0            999 V2000
10001.4291 9998.7788    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.1427 9998.3647    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.4291 9999.6028    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.149910001.6370    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10002.858310001.6370    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9996.435110001.2260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.149910002.4610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.573910001.2260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.858310002.4610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.722410001.6370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.435110002.8740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10004.287510001.6370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.573910002.8740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0023 9997.1284    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7167 9997.5409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7167 9998.3660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0023 9998.7785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2878 9998.3660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2878 9997.5409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.4311 9999.9888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.145710000.4014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.145710001.2263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.431210001.6389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0033 9999.9887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.717810000.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.717810001.2263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.003310001.6387    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
 9997.861110000.4012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5756 9999.9888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.290110000.4013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.290210001.2263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.575710001.6388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.861110001.2262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  4  6  1  0  0  0  0
  4  7  1  0  0  0  0
  5  8  1  0  0  0  0
  5  9  1  0  0  0  0
  6 10  1  0  0  0  0
  7 11  1  0  0  0  0
  8 12  1  0  0  0  0
  9 13  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 14  1  0  0  0  0
  1 16  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 22  5  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 17 24  1  0  0  0  0
 25 20  2  0  0  0  0
 23 26  2  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 28  1  0  0  0  0
 33  4  1  0  0  0  0
 27 31  2  0  0  0  0
 24 30  2  0  0  0  0
M  CHG  1  27   1
M  END
> <DATABASE_ID>
HMDB0031786

> <DATABASE_NAME>
hmdb

> <SMILES>
CCN(CC)C1=CC2=[O+]C3=CC(=CC=C3C(=C2C=C1)C1=C(C=CC=C1)C(O)=O)N(CC)CC

> <INCHI_IDENTIFIER>
InChI=1S/C28H30N2O3/c1-5-29(6-2)19-13-15-23-25(17-19)33-26-18-20(30(7-3)8-4)14-16-24(26)27(23)21-11-9-10-12-22(21)28(31)32/h9-18H,5-8H2,1-4H3/p+1

> <INCHI_KEY>
CVAVMIODJQHEEH-UHFFFAOYSA-O

> <FORMULA>
C28H31N2O3

> <MOLECULAR_WEIGHT>
443.5573

> <EXACT_MASS>
443.233467868

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
51.4643601795593

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
9-(2-carboxyphenyl)-6-(diethylamino)-N,N-diethyl-3H-xanthen-3-iminium

> <ALOGPS_LOGP>
5.95

> <JCHEM_LOGP>
1.7813270892424944

> <ALOGPS_LOGS>
-5.13

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.497490744832413

> <JCHEM_PKA_STRONGEST_BASIC>
4.343600091040459

> <JCHEM_POLAR_SURFACE_AREA>
52.78

> <JCHEM_REFRACTIVITY>
157.9201

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.53e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
rhodamine B(1+)

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0031786 (Rhodamine B)

HMDB0031786
     RDKit          3D
Rhodamine B
 64 67  0  0  0  0  0  0  0  0999 V2000
   -5.2281    3.1879   -0.9780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1693    1.7000   -1.2842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9004    0.9110   -0.1119 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7970    0.7437    0.9850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0115    1.9771    1.8160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6218    0.2385   -0.0689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5144   -1.1170   -0.1743 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2584   -1.7072   -0.1574 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1338   -0.9294   -0.0355 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1247   -1.5311   -0.0221 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2744   -2.9694   -0.1072 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2476   -3.7593    1.0511 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3494   -5.1255    1.0106 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4823   -5.7062   -0.2216 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5170   -4.9808   -1.4177 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4112   -3.6087   -1.3340 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4494   -2.8187   -2.5646 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5781   -3.4664   -3.6666 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3589   -1.4582   -2.6394 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2058   -0.7036    0.0970 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4829   -1.1734    0.1151 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5549   -0.3185    0.2299 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3739    1.0435    0.3309 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4704    1.9369    0.4287 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2001    2.0232    1.6655 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6672    1.0279    2.6492 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    2.7510   -0.7165 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1157    2.3582   -1.3362 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0786    1.5344    0.3142 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0026    0.6793    0.1983 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1799    1.2128    0.1853 O   0  0  0  0  0  3  0  0  0  0  0  0
   -1.2542    0.4374    0.0699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5036    1.0162    0.0537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3091    3.5814   -0.5437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1561    3.4340   -0.4195 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3549    3.7005   -1.9754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0901    1.4036   -1.7789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3572    1.6015   -2.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4388   -0.0600    1.6603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7559    0.3581    0.5558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0032    2.4415    1.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1646    2.6920    1.7425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0370    1.7174    2.9203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3943   -1.7110   -0.2726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1094   -2.7738   -0.2345 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1417   -3.2615    2.0009 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3254   -5.7322    1.9264 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5629   -6.7883   -0.3053 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6244   -5.4999   -2.3831 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5289   -0.9733   -3.5043 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6291   -2.2588    0.0348 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5600   -0.7502    0.2333 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0657    3.0581    2.1268 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3001    1.9634    1.5086 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9627    1.3071    3.7035 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1427    0.0329    2.4083 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5778    0.9445    2.5333 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9890    2.7091   -1.4587 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9146    3.8433   -0.3856 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6003    1.5806   -0.7476 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9402    2.0468   -2.3984 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7644    3.2665   -1.4119 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9048    2.6172    0.3931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5469    2.1039    0.1385 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  3  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 17 19  1  0
 10 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 24 27  1  0
 27 28  1  0
 23 29  2  0
 29 30  1  0
 30 31  2  0
 31 32  1  0
 32 33  2  0
 33  6  1  0
 32  9  1  0
 16 11  1  0
 30 20  1  0
  1 34  1  0
  1 35  1  0
  1 36  1  0
  2 37  1  0
  2 38  1  0
  4 39  1  0
  4 40  1  0
  5 41  1  0
  5 42  1  0
  5 43  1  0
  7 44  1  0
  8 45  1  0
 12 46  1  0
 13 47  1  0
 14 48  1  0
 15 49  1  0
 19 50  1  0
 21 51  1  0
 22 52  1  0
 25 53  1  0
 25 54  1  0
 26 55  1  0
 26 56  1  0
 26 57  1  0
 27 58  1  0
 27 59  1  0
 28 60  1  0
 28 61  1  0
 28 62  1  0
 29 63  1  0
 33 64  1  0
M  CHG  1  31   1
M  END
Download

PDB for HMDB0031786 (Rhodamine B)

HEADER    PROTEIN                                 24-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-20         0                                  
HETATM    1  C   UNK     0    8669.3348664.387   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8670.6668663.614   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8669.3348665.925   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0    8661.3468669.722   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0    8672.0028669.722   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0    8660.0128668.955   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8661.3468671.261   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8673.3388668.955   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8672.0028671.261   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8658.6828669.722   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8660.0128672.031   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8674.6708669.722   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8673.3388672.031   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8666.6718661.306   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8668.0058662.076   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8668.0058663.617   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8666.6718664.387   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8665.3378663.617   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8665.3378662.076   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8669.3388666.646   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8670.6728667.416   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8670.6728668.956   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8669.3388669.726   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0    8666.6738666.646   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0    8668.0078667.416   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0    8668.0078668.956   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0    8666.6738669.726   0.000  0.00  0.00           O+1
HETATM   28  C   UNK     0    8662.6748667.416   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0    8664.0088666.646   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0    8665.3428667.416   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0    8665.3428668.956   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0    8664.0088669.726   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0    8662.6748668.956   0.000  0.00  0.00           C+0
CONECT    1    2    3   16                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    6    7   33                                                  
CONECT    5    8    9   22                                                  
CONECT    6    4   10                                                       
CONECT    7    4   11                                                       
CONECT    8    5   12                                                       
CONECT    9    5   13                                                       
CONECT   10    6                                                            
CONECT   11    7                                                            
CONECT   12    8                                                            
CONECT   13    9                                                            
CONECT   14   15   19                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17    1                                                  
CONECT   17   16   18   24                                                  
CONECT   18   17   19                                                       
CONECT   19   18   14                                                       
CONECT   20   21   25                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23    5                                                  
CONECT   23   22   26                                                       
CONECT   24   25   17   30                                                  
CONECT   25   24   26   20                                                  
CONECT   26   25   27   23                                                  
CONECT   27   26   31                                                       
CONECT   28   29   33                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   24                                                  
CONECT   31   30   32   27                                                  
CONECT   32   31   33                                                       
CONECT   33   32   28    4                                                  
MASTER        0    0    0    0    0    0    0    0   33    0   72    0
END
Download

3D PDB for HMDB0031786 (Rhodamine B)

COMPND    HMDB0031786
HETATM    1  C1  UNL     1      -5.228   3.188  -0.978  1.00  0.00           C  
HETATM    2  C2  UNL     1      -5.169   1.700  -1.284  1.00  0.00           C  
HETATM    3  N1  UNL     1      -4.900   0.911  -0.112  1.00  0.00           N  
HETATM    4  C3  UNL     1      -5.797   0.744   0.985  1.00  0.00           C  
HETATM    5  C4  UNL     1      -6.011   1.977   1.816  1.00  0.00           C  
HETATM    6  C5  UNL     1      -3.622   0.239  -0.069  1.00  0.00           C  
HETATM    7  C6  UNL     1      -3.514  -1.117  -0.174  1.00  0.00           C  
HETATM    8  C7  UNL     1      -2.258  -1.707  -0.157  1.00  0.00           C  
HETATM    9  C8  UNL     1      -1.134  -0.929  -0.036  1.00  0.00           C  
HETATM   10  C9  UNL     1       0.125  -1.531  -0.022  1.00  0.00           C  
HETATM   11  C10 UNL     1       0.274  -2.969  -0.107  1.00  0.00           C  
HETATM   12  C11 UNL     1       0.248  -3.759   1.051  1.00  0.00           C  
HETATM   13  C12 UNL     1       0.349  -5.126   1.011  1.00  0.00           C  
HETATM   14  C13 UNL     1       0.482  -5.706  -0.222  1.00  0.00           C  
HETATM   15  C14 UNL     1       0.517  -4.981  -1.418  1.00  0.00           C  
HETATM   16  C15 UNL     1       0.411  -3.609  -1.334  1.00  0.00           C  
HETATM   17  C16 UNL     1       0.449  -2.819  -2.565  1.00  0.00           C  
HETATM   18  O1  UNL     1       0.578  -3.466  -3.667  1.00  0.00           O  
HETATM   19  O2  UNL     1       0.359  -1.458  -2.639  1.00  0.00           O  
HETATM   20  C17 UNL     1       1.206  -0.704   0.097  1.00  0.00           C  
HETATM   21  C18 UNL     1       2.483  -1.173   0.115  1.00  0.00           C  
HETATM   22  C19 UNL     1       3.555  -0.318   0.230  1.00  0.00           C  
HETATM   23  C20 UNL     1       3.374   1.044   0.331  1.00  0.00           C  
HETATM   24  N2  UNL     1       4.470   1.937   0.429  1.00  0.00           N  
HETATM   25  C21 UNL     1       5.200   2.023   1.666  1.00  0.00           C  
HETATM   26  C22 UNL     1       4.667   1.028   2.649  1.00  0.00           C  
HETATM   27  C23 UNL     1       4.810   2.751  -0.717  1.00  0.00           C  
HETATM   28  C24 UNL     1       6.116   2.358  -1.336  1.00  0.00           C  
HETATM   29  C25 UNL     1       2.079   1.534   0.314  1.00  0.00           C  
HETATM   30  C26 UNL     1       1.003   0.679   0.198  1.00  0.00           C  
HETATM   31  O3  UNL     1      -0.180   1.213   0.185  1.00  0.00           O1+
HETATM   32  C27 UNL     1      -1.254   0.437   0.070  1.00  0.00           C  
HETATM   33  C28 UNL     1      -2.504   1.016   0.054  1.00  0.00           C  
HETATM   34  H1  UNL     1      -4.309   3.581  -0.544  1.00  0.00           H  
HETATM   35  H2  UNL     1      -6.156   3.434  -0.419  1.00  0.00           H  
HETATM   36  H3  UNL     1      -5.355   3.701  -1.975  1.00  0.00           H  
HETATM   37  H4  UNL     1      -6.090   1.404  -1.779  1.00  0.00           H  
HETATM   38  H5  UNL     1      -4.357   1.602  -2.052  1.00  0.00           H  
HETATM   39  H6  UNL     1      -5.439  -0.060   1.660  1.00  0.00           H  
HETATM   40  H7  UNL     1      -6.756   0.358   0.556  1.00  0.00           H  
HETATM   41  H8  UNL     1      -7.003   2.441   1.621  1.00  0.00           H  
HETATM   42  H9  UNL     1      -5.165   2.692   1.743  1.00  0.00           H  
HETATM   43  H10 UNL     1      -6.037   1.717   2.920  1.00  0.00           H  
HETATM   44  H11 UNL     1      -4.394  -1.711  -0.273  1.00  0.00           H  
HETATM   45  H12 UNL     1      -2.109  -2.774  -0.235  1.00  0.00           H  
HETATM   46  H13 UNL     1       0.142  -3.261   2.001  1.00  0.00           H  
HETATM   47  H14 UNL     1       0.325  -5.732   1.926  1.00  0.00           H  
HETATM   48  H15 UNL     1       0.563  -6.788  -0.305  1.00  0.00           H  
HETATM   49  H16 UNL     1       0.624  -5.500  -2.383  1.00  0.00           H  
HETATM   50  H17 UNL     1       0.529  -0.973  -3.504  1.00  0.00           H  
HETATM   51  H18 UNL     1       2.629  -2.259   0.035  1.00  0.00           H  
HETATM   52  H19 UNL     1       4.560  -0.750   0.233  1.00  0.00           H  
HETATM   53  H20 UNL     1       5.066   3.058   2.127  1.00  0.00           H  
HETATM   54  H21 UNL     1       6.300   1.963   1.509  1.00  0.00           H  
HETATM   55  H22 UNL     1       4.963   1.307   3.704  1.00  0.00           H  
HETATM   56  H23 UNL     1       5.143   0.033   2.408  1.00  0.00           H  
HETATM   57  H24 UNL     1       3.578   0.944   2.533  1.00  0.00           H  
HETATM   58  H25 UNL     1       3.989   2.709  -1.459  1.00  0.00           H  
HETATM   59  H26 UNL     1       4.915   3.843  -0.386  1.00  0.00           H  
HETATM   60  H27 UNL     1       6.600   1.581  -0.748  1.00  0.00           H  
HETATM   61  H28 UNL     1       5.940   2.047  -2.398  1.00  0.00           H  
HETATM   62  H29 UNL     1       6.764   3.266  -1.412  1.00  0.00           H  
HETATM   63  H30 UNL     1       1.905   2.617   0.393  1.00  0.00           H  
HETATM   64  H31 UNL     1      -2.547   2.104   0.139  1.00  0.00           H  
CONECT    1    2   34   35   36
CONECT    2    3   37   38
CONECT    3    4    6
CONECT    4    5   39   40
CONECT    5   41   42   43
CONECT    6    7    7   33
CONECT    7    8   44
CONECT    8    9    9   45
CONECT    9   10   32
CONECT   10   11   20   20
CONECT   11   12   12   16
CONECT   12   13   46
CONECT   13   14   14   47
CONECT   14   15   48
CONECT   15   16   16   49
CONECT   16   17
CONECT   17   18   18   19
CONECT   19   50
CONECT   20   21   30
CONECT   21   22   22   51
CONECT   22   23   52
CONECT   23   24   29   29
CONECT   24   25   27
CONECT   25   26   53   54
CONECT   26   55   56   57
CONECT   27   28   58   59
CONECT   28   60   61   62
CONECT   29   30   63
CONECT   30   31   31
CONECT   31   32
CONECT   32   33   33
CONECT   33   64
END
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SMILES for HMDB0031786 (Rhodamine B)

CCN(CC)C1=CC2=[O+]C3=CC(=CC=C3C(=C2C=C1)C1=C(C=CC=C1)C(O)=O)N(CC)CC
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INCHI for HMDB0031786 (Rhodamine B)

InChI=1S/C28H30N2O3/c1-5-29(6-2)19-13-15-23-25(17-19)33-26-18-20(30(7-3)8-4)14-16-24(26)27(23)21-11-9-10-12-22(21)28(31)32/h9-18H,5-8H2,1-4H3/p+1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
N-[9-(2-Carboxyphenyl)-6-(diethylamino)-3H-xanthen-3-ylidene]-N-ethylethanaminiumChEBI
Rhodamine b cationChEBI
81-88-9 (CHLORIDE)HMDB
9-(2-Carboxyphenyl)-3,6-bis(diethylamino)-xanthyliumHMDB
9-(2-Carboxyphenyl)-3,6-bis(diethylamino)xanthyliumHMDB
9-(2-Carboxyphenyl)-3,6-bis(diethylamino)xanthylium(1+), 9ciHMDB
Basazol red 71PHMDB
Basic rose redHMDB
Basic violet 10HMDB
C.I. 45170HMDB
C.I. basic violet 10HMDB
C.I. FOOD red 15HMDB
C.I. solvent red 49HMDB
Calcozine red BXHMDB
Calcozine rhodamine BXPHMDB
Cerise toner X 1127HMDB
D And C red 19HMDB
Eriosin rhodamine bHMDB
FOOD Red 15HMDB
N-[9-(2-Carboxyphenyl)-6-(diethylamino)-3H-xanthen-3-ylidene]-N-ethylethanaminium(1+), 9ciHMDB
Pilot 578HMDB
RhodamineHMDB
Rhodamine 610HMDB
Rhodamine b monocationHMDB
Rhodamine b(1+)HMDB
Rhodamine lake red bHMDB
TetraethylrhodamineHMDB
RhodaminesHMDB
Rhodamine bHMDB
Chemical FormulaC28H31N2O3
Average Molecular Weight443.5573
Monoisotopic Molecular Weight443.233467868
IUPAC Name9-(2-carboxyphenyl)-6-(diethylamino)-N,N-diethyl-3H-xanthen-3-iminium
Traditional Namerhodamine B(1+)
CAS Registry Number64381-98-2
SMILES
CCN(CC)C1=CC2=[O+]C3=CC(=CC=C3C(=C2C=C1)C1=C(C=CC=C1)C(O)=O)N(CC)CC
InChI Identifier
InChI=1S/C28H30N2O3/c1-5-29(6-2)19-13-15-23-25(17-19)33-26-18-20(30(7-3)8-4)14-16-24(26)27(23)21-11-9-10-12-22(21)28(31)32/h9-18H,5-8H2,1-4H3/p+1
InChI KeyCVAVMIODJQHEEH-UHFFFAOYSA-O
Chemical Taxonomy
Description Belongs to the class of organic compounds known as xanthenes. These are polycyclic aromatic compounds containing a xanthene moiety, which consists of two benzene rings joined to each other by a pyran ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzopyrans
Sub Class1-benzopyrans
Direct ParentXanthenes
Alternative Parents
Substituents
  • Xanthene
  • Benzoic acid or derivatives
  • Benzoic acid
  • Benzoyl
  • Tertiary aliphatic/aromatic amine
  • Dialkylarylamine
  • Monocyclic benzene moiety
  • Benzenoid
  • Heteroaromatic compound
  • Amino acid or derivatives
  • Amino acid
  • Tertiary amine
  • Oxacycle
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Amine
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.00046 g/LALOGPS
logP5.95ALOGPS
logP1.78ChemAxon
logS-5.1ALOGPS
pKa (Strongest Acidic)3.5ChemAxon
pKa (Strongest Basic)4.34ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area52.78 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity157.92 m³·mol⁻¹ChemAxon
Polarizability51.46 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+204.79431661259
DarkChem[M-H]-202.59631661259
DeepCCS[M+H]+210.15430932474
DeepCCS[M-H]-207.75830932474
DeepCCS[M-2H]-240.64230932474
DeepCCS[M+Na]+216.06630932474
AllCCS[M+H]+206.832859911
AllCCS[M+H-H2O]+204.432859911
AllCCS[M+NH4]+208.932859911
AllCCS[M+Na]+209.532859911
AllCCS[M-H]-209.832859911
AllCCS[M+Na-2H]-210.332859911
AllCCS[M+HCOO]-211.132859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.6.95 minutes32390414
Predicted by Siyang on May 30, 202220.9719 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.91 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid32.7 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid3002.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid483.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid270.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid240.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid258.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid758.2 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid786.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)86.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1840.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid719.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1684.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid605.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid518.9 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate243.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA241.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water8.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Rhodamine BCCN(CC)C1=CC2=[O+]C3=CC(=CC=C3C(=C2C=C1)C1=C(C=CC=C1)C(O)=O)N(CC)CC4921.0Standard polar33892256
Rhodamine BCCN(CC)C1=CC2=[O+]C3=CC(=CC=C3C(=C2C=C1)C1=C(C=CC=C1)C(O)=O)N(CC)CC3640.5Standard non polar33892256
Rhodamine BCCN(CC)C1=CC2=[O+]C3=CC(=CC=C3C(=C2C=C1)C1=C(C=CC=C1)C(O)=O)N(CC)CC3938.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Rhodamine B,1TMS,isomer #1CCN(CC)C1=CC=C2C(C3=CC=CC=C3C(=O)O[Si](C)(C)C)=C3C=CC(N(CC)CC)=CC3=[O+]C2=C13682.8Semi standard non polar33892256
Rhodamine B,1TBDMS,isomer #1CCN(CC)C1=CC=C2C(C3=CC=CC=C3C(=O)O[Si](C)(C)C(C)(C)C)=C3C=CC(N(CC)CC)=CC3=[O+]C2=C13876.0Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008459
KNApSAcK IDNot Available
Chemspider ID6440
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkRhodamine B
METLIN IDNot Available
PubChem Compound6695
PDB IDNot Available
ChEBI ID52896
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Wang M, Nie X, Tian L, Hu J, Yin D, Qiao H, Li T, Li Y: Rhodamine B in spices determined by a sensitive UPLC-MS/MS method. Food Addit Contam Part B Surveill. 2019 Mar;12(1):59-64. doi: 10.1080/19393210.2018.1548504. Epub 2018 Nov 21. [PubMed:30463493 ]
  2. Johnson BJ, Mitchell SN, Paton CJ, Stevenson J, Staunton KM, Snoad N, Beebe N, White BJ, Ritchie SA: Use of rhodamine B to mark the body and seminal fluid of male Aedes aegypti for mark-release-recapture experiments and estimating efficacy of sterile male releases. PLoS Negl Trop Dis. 2017 Sep 28;11(9):e0005902. doi: 10.1371/journal.pntd.0005902. eCollection 2017 Sep. [PubMed:28957318 ]
  3. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .