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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:11:49 UTC

Update Date

2021-09-26 22:55:02 UTC

HMDB ID

HMDB0246161

Secondary Accession Numbers

None

Metabolite Identification

Common Name

(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate

Description

(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate belongs to the class of organic compounds known as pyrimidinecarboxylic acids. These are pyrimidines with a structure containing a carboxyl group attached to the pyrimidine ring. Based on a literature review very few articles have been published on (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate. This compound has been identified in human blood as reported by (PMID: 31557052 ). (s)-ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652309112101122D          

 29 31  0  0  0  0            999 V2000
   -3.4656    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512   -0.0616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222   -0.0616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367   -1.2991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222   -1.7116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222   -2.5366    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367   -2.9491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512   -2.5366    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512   -1.7116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4656   -1.2991    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4656   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1801   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8946   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6091   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6091    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8946    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1801    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3235    1.1759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3235    2.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3235   -0.4741    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367   -3.7741    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3693   -4.2590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6242   -5.0437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4492   -5.0437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7041   -4.2590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4888   -4.0041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1019   -4.5561    0.0000 O   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
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 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  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
 14 19  1  0  0  0  0
 17 20  1  0  0  0  0
 20 21  1  0  0  0  0
 16 22  1  0  0  0  0
  9 23  1  0  0  0  0
 23 24  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
 23 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
M  END

HMDB0246161
     RDKit          3D
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-...
 54 56  0  0  0  0  0  0  0  0999 V2000
   -0.7964    6.7952    0.6607 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4340    6.0279    1.0819 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3096    4.6958    0.6302 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7126    3.8885    1.0214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5466    4.4498    1.8340 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9694    2.5099    0.6442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1022    1.8930    1.1929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3698    0.6317    0.8728 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6158   -0.1003    0.0471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9729   -1.4456   -0.2417 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3107   -2.3965   -1.1089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4088   -3.2903   -1.6210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5621   -3.1407   -0.6850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1191   -2.1204    0.3172 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7005   -2.8164    1.6185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7054   -3.7260    1.3150 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5399    0.4941   -0.4706 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1813    1.7893   -0.2010 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9676    2.3404   -0.7920 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7304    1.4636   -1.6762 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2561    0.2760   -0.9793 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8161   -0.7140   -1.7665 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3470   -1.8772   -1.2321 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3187   -2.0608    0.1383 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8431   -3.2144    0.6909 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4195   -4.2431   -0.0590 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7597   -1.0715    0.9194 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7128   -1.2848    2.6667 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.2344    0.0832    0.3696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5115    6.7653    1.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5448    7.8588    0.4823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2651    6.3617   -0.2453 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3669    6.4866    0.6669 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5300    6.0947    2.1941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7508    2.4241    1.8636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5673   -3.0245   -0.5965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8745   -1.8568   -1.9838 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7451   -2.9413   -2.6396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0716   -4.3383   -1.7638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7822   -4.1309   -0.1910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5072   -2.8452   -1.2233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9294   -1.4095    0.5947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6051   -3.3134    2.0055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3407   -1.9978    2.2862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405   -4.5633    1.8073 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2599    3.3022   -0.6179 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5683    2.0047   -2.1572 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0252    1.1625   -2.4799 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8505   -0.5925   -2.8541 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7671   -2.6036   -1.9210 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9655   -4.9773    0.5320 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6071   -4.7816   -0.5981 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0554   -3.7659   -0.8525 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8043    0.8448    0.9965 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  2  0
  4  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  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
  9 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 23 24  2  0
 24 25  1  0
 25 26  1  0
 24 27  1  0
 27 28  1  0
 27 29  2  0
 18  6  1  0
 29 21  1  0
 14 10  1  0
  1 30  1  0
  1 31  1  0
  1 32  1  0
  2 33  1  0
  2 34  1  0
  7 35  1  0
 11 36  1  0
 11 37  1  0
 12 38  1  0
 12 39  1  0
 13 40  1  0
 13 41  1  0
 14 42  1  0
 15 43  1  0
 15 44  1  0
 16 45  1  0
 19 46  1  0
 20 47  1  0
 20 48  1  0
 22 49  1  0
 23 50  1  0
 26 51  1  0
 26 52  1  0
 26 53  1  0
 29 54  1  0
M  END


  Mrv1652309112101122D          

 29 31  0  0  0  0            999 V2000
   -3.4656    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512   -0.0616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222   -0.0616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367   -1.2991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222   -1.7116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222   -2.5366    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367   -2.9491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512   -2.5366    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512   -1.7116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4656   -1.2991    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4656   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1801   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8946   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6091   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6091    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8946    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1801    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3235    1.1759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3235    2.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3235   -0.4741    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367   -3.7741    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3693   -4.2590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6242   -5.0437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4492   -5.0437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7041   -4.2590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4888   -4.0041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1019   -4.5561    0.0000 O   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
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 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  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
 14 19  1  0  0  0  0
 17 20  1  0  0  0  0
 20 21  1  0  0  0  0
 16 22  1  0  0  0  0
  9 23  1  0  0  0  0
 23 24  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
 23 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246161

> <DATABASE_NAME>
hmdb

> <SMILES>
CCOC(=O)C1=CN=C(N=C1NCC1=CC(Cl)=C(OC)C=C1)N1CCCC1CO

> <INCHI_IDENTIFIER>
InChI=1S/C20H25ClN4O4/c1-3-29-19(27)15-11-23-20(25-8-4-5-14(25)12-26)24-18(15)22-10-13-6-7-17(28-2)16(21)9-13/h6-7,9,11,14,26H,3-5,8,10,12H2,1-2H3,(H,22,23,24)

> <INCHI_KEY>
NUTJUOHYJBWTSH-UHFFFAOYSA-N

> <FORMULA>
C20H25ClN4O4

> <MOLECULAR_WEIGHT>
420.89

> <EXACT_MASS>
420.156433

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
44.51786272295406

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
ethyl 4-{[(3-chloro-4-methoxyphenyl)methyl]amino}-2-[2-(hydroxymethyl)pyrrolidin-1-yl]pyrimidine-5-carboxylate

> <ALOGPS_LOGP>
3.12

> <JCHEM_LOGP>
3.8603949653333345

> <ALOGPS_LOGS>
-3.77

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.718958567441806

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.975245045351436

> <JCHEM_PKA_STRONGEST_BASIC>
5.202849859215287

> <JCHEM_POLAR_SURFACE_AREA>
96.81

> <JCHEM_REFRACTIVITY>
113.76219999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.08e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ethyl 4-{[(3-chloro-4-methoxyphenyl)methyl]amino}-2-[2-(hydroxymethyl)pyrrolidin-1-yl]pyrimidine-5-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0246161
     RDKit          3D
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-...
 54 56  0  0  0  0  0  0  0  0999 V2000
   -0.7964    6.7952    0.6607 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4340    6.0279    1.0819 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3096    4.6958    0.6302 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7126    3.8885    1.0214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5466    4.4498    1.8340 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9694    2.5099    0.6442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1022    1.8930    1.1929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3698    0.6317    0.8728 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6158   -0.1003    0.0471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9729   -1.4456   -0.2417 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3107   -2.3965   -1.1089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4088   -3.2903   -1.6210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5621   -3.1407   -0.6850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1191   -2.1204    0.3172 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7005   -2.8164    1.6185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7054   -3.7260    1.3150 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5399    0.4941   -0.4706 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1813    1.7893   -0.2010 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9676    2.3404   -0.7920 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7304    1.4636   -1.6762 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2561    0.2760   -0.9793 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8161   -0.7140   -1.7665 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3470   -1.8772   -1.2321 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3187   -2.0608    0.1383 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8431   -3.2144    0.6909 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4195   -4.2431   -0.0590 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7597   -1.0715    0.9194 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7128   -1.2848    2.6667 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.2344    0.0832    0.3696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5115    6.7653    1.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5448    7.8588    0.4823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2651    6.3617   -0.2453 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3669    6.4866    0.6669 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5300    6.0947    2.1941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7508    2.4241    1.8636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5673   -3.0245   -0.5965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8745   -1.8568   -1.9838 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7451   -2.9413   -2.6396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0716   -4.3383   -1.7638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7822   -4.1309   -0.1910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5072   -2.8452   -1.2233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9294   -1.4095    0.5947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6051   -3.3134    2.0055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3407   -1.9978    2.2862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405   -4.5633    1.8073 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2599    3.3022   -0.6179 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5683    2.0047   -2.1572 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0252    1.1625   -2.4799 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8505   -0.5925   -2.8541 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7671   -2.6036   -1.9210 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9655   -4.9773    0.5320 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6071   -4.7816   -0.5981 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0554   -3.7659   -0.8525 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8043    0.8448    0.9965 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  2  0
  4  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  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
  9 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 23 24  2  0
 24 25  1  0
 25 26  1  0
 24 27  1  0
 27 28  1  0
 27 29  2  0
 18  6  1  0
 29 21  1  0
 14 10  1  0
  1 30  1  0
  1 31  1  0
  1 32  1  0
  2 33  1  0
  2 34  1  0
  7 35  1  0
 11 36  1  0
 11 37  1  0
 12 38  1  0
 12 39  1  0
 13 40  1  0
 13 41  1  0
 14 42  1  0
 15 43  1  0
 15 44  1  0
 16 45  1  0
 19 46  1  0
 20 47  1  0
 20 48  1  0
 22 49  1  0
 23 50  1  0
 26 51  1  0
 26 52  1  0
 26 53  1  0
 29 54  1  0
M  END

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -6.469   2.195   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.136   1.425   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -5.136  -0.115   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -3.802  -0.885   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -2.468  -0.115   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -3.802  -2.425   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.468  -3.195   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -2.468  -4.735   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -3.802  -5.505   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -5.136  -4.735   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -5.136  -3.195   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -6.469  -2.425   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -6.469  -0.885   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -7.803  -0.115   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -9.137  -0.885   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -10.470  -0.115   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -10.470   1.425   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -9.137   2.195   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -7.803   1.425   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0     -11.804   2.195   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0     -11.804   3.735   0.000  0.00  0.00           C+0
HETATM   22 Cl   UNK     0     -11.804  -0.885   0.000  0.00  0.00          Cl+0
HETATM   23  N   UNK     0      -3.802  -7.045   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0      -2.556  -7.950   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.032  -9.415   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -4.572  -9.415   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -5.048  -7.950   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -6.512  -7.474   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -7.657  -8.505   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   23                                                  
CONECT   10    9   11                                                       
CONECT   11   10    6   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   22                                                  
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18   14                                                       
CONECT   20   17   21                                                       
CONECT   21   20                                                            
CONECT   22   16                                                            
CONECT   23    9   24   27                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   23   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   62    0
END

COMPND    HMDB0246161
HETATM    1  C1  UNL     1      -0.796   6.795   0.661  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.434   6.028   1.082  1.00  0.00           C  
HETATM    3  O1  UNL     1       0.310   4.696   0.630  1.00  0.00           O  
HETATM    4  C3  UNL     1      -0.713   3.888   1.021  1.00  0.00           C  
HETATM    5  O2  UNL     1      -1.547   4.450   1.834  1.00  0.00           O  
HETATM    6  C4  UNL     1      -0.969   2.510   0.644  1.00  0.00           C  
HETATM    7  C5  UNL     1      -2.102   1.893   1.193  1.00  0.00           C  
HETATM    8  N1  UNL     1      -2.370   0.632   0.873  1.00  0.00           N  
HETATM    9  C6  UNL     1      -1.616  -0.100   0.047  1.00  0.00           C  
HETATM   10  N2  UNL     1      -1.973  -1.446  -0.242  1.00  0.00           N  
HETATM   11  C7  UNL     1      -1.311  -2.396  -1.109  1.00  0.00           C  
HETATM   12  C8  UNL     1      -2.409  -3.290  -1.621  1.00  0.00           C  
HETATM   13  C9  UNL     1      -3.562  -3.141  -0.685  1.00  0.00           C  
HETATM   14  C10 UNL     1      -3.119  -2.120   0.317  1.00  0.00           C  
HETATM   15  C11 UNL     1      -2.701  -2.816   1.619  1.00  0.00           C  
HETATM   16  O3  UNL     1      -1.705  -3.726   1.315  1.00  0.00           O  
HETATM   17  N3  UNL     1      -0.540   0.494  -0.471  1.00  0.00           N  
HETATM   18  C12 UNL     1      -0.181   1.789  -0.201  1.00  0.00           C  
HETATM   19  N4  UNL     1       0.968   2.340  -0.792  1.00  0.00           N  
HETATM   20  C13 UNL     1       1.730   1.464  -1.676  1.00  0.00           C  
HETATM   21  C14 UNL     1       2.256   0.276  -0.979  1.00  0.00           C  
HETATM   22  C15 UNL     1       2.816  -0.714  -1.766  1.00  0.00           C  
HETATM   23  C16 UNL     1       3.347  -1.877  -1.232  1.00  0.00           C  
HETATM   24  C17 UNL     1       3.319  -2.061   0.138  1.00  0.00           C  
HETATM   25  O4  UNL     1       3.843  -3.214   0.691  1.00  0.00           O  
HETATM   26  C18 UNL     1       4.419  -4.243  -0.059  1.00  0.00           C  
HETATM   27  C19 UNL     1       2.760  -1.071   0.919  1.00  0.00           C  
HETATM   28 CL1  UNL     1       2.713  -1.285   2.667  1.00  0.00          CL  
HETATM   29  C20 UNL     1       2.234   0.083   0.370  1.00  0.00           C  
HETATM   30  H1  UNL     1      -1.512   6.765   1.508  1.00  0.00           H  
HETATM   31  H2  UNL     1      -0.545   7.859   0.482  1.00  0.00           H  
HETATM   32  H3  UNL     1      -1.265   6.362  -0.245  1.00  0.00           H  
HETATM   33  H4  UNL     1       1.367   6.487   0.667  1.00  0.00           H  
HETATM   34  H5  UNL     1       0.530   6.095   2.194  1.00  0.00           H  
HETATM   35  H6  UNL     1      -2.751   2.424   1.864  1.00  0.00           H  
HETATM   36  H7  UNL     1      -0.567  -3.024  -0.597  1.00  0.00           H  
HETATM   37  H8  UNL     1      -0.875  -1.857  -1.984  1.00  0.00           H  
HETATM   38  H9  UNL     1      -2.745  -2.941  -2.640  1.00  0.00           H  
HETATM   39  H10 UNL     1      -2.072  -4.338  -1.764  1.00  0.00           H  
HETATM   40  H11 UNL     1      -3.782  -4.131  -0.191  1.00  0.00           H  
HETATM   41  H12 UNL     1      -4.507  -2.845  -1.223  1.00  0.00           H  
HETATM   42  H13 UNL     1      -3.929  -1.409   0.595  1.00  0.00           H  
HETATM   43  H14 UNL     1      -3.605  -3.313   2.006  1.00  0.00           H  
HETATM   44  H15 UNL     1      -2.341  -1.998   2.286  1.00  0.00           H  
HETATM   45  H16 UNL     1      -1.840  -4.563   1.807  1.00  0.00           H  
HETATM   46  H17 UNL     1       1.260   3.302  -0.618  1.00  0.00           H  
HETATM   47  H18 UNL     1       2.568   2.005  -2.157  1.00  0.00           H  
HETATM   48  H19 UNL     1       1.025   1.162  -2.480  1.00  0.00           H  
HETATM   49  H20 UNL     1       2.851  -0.593  -2.854  1.00  0.00           H  
HETATM   50  H21 UNL     1       3.767  -2.604  -1.921  1.00  0.00           H  
HETATM   51  H22 UNL     1       4.966  -4.977   0.532  1.00  0.00           H  
HETATM   52  H23 UNL     1       3.607  -4.782  -0.598  1.00  0.00           H  
HETATM   53  H24 UNL     1       5.055  -3.766  -0.853  1.00  0.00           H  
HETATM   54  H25 UNL     1       1.804   0.845   0.997  1.00  0.00           H  
CONECT    1    2   30   31   32
CONECT    2    3   33   34
CONECT    3    4
CONECT    4    5    5    6
CONECT    6    7    7   18
CONECT    7    8   35
CONECT    8    9    9
CONECT    9   10   17
CONECT   10   11   14
CONECT   11   12   36   37
CONECT   12   13   38   39
CONECT   13   14   40   41
CONECT   14   15   42
CONECT   15   16   43   44
CONECT   16   45
CONECT   17   18   18
CONECT   18   19
CONECT   19   20   46
CONECT   20   21   47   48
CONECT   21   22   22   29
CONECT   22   23   49
CONECT   23   24   24   50
CONECT   24   25   27
CONECT   25   26
CONECT   26   51   52   53
CONECT   27   28   29   29
CONECT   29   54
END

HMDB0246161
     RDKit          3D
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-...
 54 56  0  0  0  0  0  0  0  0999 V2000
   -0.7964    6.7952    0.6607 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4340    6.0279    1.0819 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3096    4.6958    0.6302 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7126    3.8885    1.0214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5466    4.4498    1.8340 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9694    2.5099    0.6442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1022    1.8930    1.1929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3698    0.6317    0.8728 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6158   -0.1003    0.0471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9729   -1.4456   -0.2417 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3107   -2.3965   -1.1089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4088   -3.2903   -1.6210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5621   -3.1407   -0.6850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1191   -2.1204    0.3172 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7005   -2.8164    1.6185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7054   -3.7260    1.3150 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5399    0.4941   -0.4706 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1813    1.7893   -0.2010 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9676    2.3404   -0.7920 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7304    1.4636   -1.6762 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2561    0.2760   -0.9793 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8161   -0.7140   -1.7665 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3470   -1.8772   -1.2321 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3187   -2.0608    0.1383 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8431   -3.2144    0.6909 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4195   -4.2431   -0.0590 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7597   -1.0715    0.9194 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7128   -1.2848    2.6667 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.2344    0.0832    0.3696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5115    6.7653    1.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5448    7.8588    0.4823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2651    6.3617   -0.2453 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3669    6.4866    0.6669 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5300    6.0947    2.1941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7508    2.4241    1.8636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5673   -3.0245   -0.5965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8745   -1.8568   -1.9838 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7451   -2.9413   -2.6396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0716   -4.3383   -1.7638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7822   -4.1309   -0.1910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5072   -2.8452   -1.2233 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9294   -1.4095    0.5947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6051   -3.3134    2.0055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3407   -1.9978    2.2862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405   -4.5633    1.8073 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2599    3.3022   -0.6179 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5683    2.0047   -2.1572 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0252    1.1625   -2.4799 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8505   -0.5925   -2.8541 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7671   -2.6036   -1.9210 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9655   -4.9773    0.5320 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6071   -4.7816   -0.5981 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0554   -3.7659   -0.8525 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8043    0.8448    0.9965 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  2  0
  4  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  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
  9 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 23 24  2  0
 24 25  1  0
 25 26  1  0
 24 27  1  0
 27 28  1  0
 27 29  2  0
 18  6  1  0
 29 21  1  0
 14 10  1  0
  1 30  1  0
  1 31  1  0
  1 32  1  0
  2 33  1  0
  2 34  1  0
  7 35  1  0
 11 36  1  0
 11 37  1  0
 12 38  1  0
 12 39  1  0
 13 40  1  0
 13 41  1  0
 14 42  1  0
 15 43  1  0
 15 44  1  0
 16 45  1  0
 19 46  1  0
 20 47  1  0
 20 48  1  0
 22 49  1  0
 23 50  1  0
 26 51  1  0
 26 52  1  0
 26 53  1  0
 29 54  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylic acid	Generator

Chemical Formula

C₂₀H₂₅ClN₄O₄

Average Molecular Weight

420.89

Monoisotopic Molecular Weight

420.156433

IUPAC Name

ethyl 4-{[(3-chloro-4-methoxyphenyl)methyl]amino}-2-[2-(hydroxymethyl)pyrrolidin-1-yl]pyrimidine-5-carboxylate

Traditional Name

ethyl 4-{[(3-chloro-4-methoxyphenyl)methyl]amino}-2-[2-(hydroxymethyl)pyrrolidin-1-yl]pyrimidine-5-carboxylate

CAS Registry Number

Not Available

SMILES

CCOC(=O)C1=CN=C(N=C1NCC1=CC(Cl)=C(OC)C=C1)N1CCCC1CO

InChI Identifier

InChI=1S/C20H25ClN4O4/c1-3-29-19(27)15-11-23-20(25-8-4-5-14(25)12-26)24-18(15)22-10-13-6-7-17(28-2)16(21)9-13/h6-7,9,11,14,26H,3-5,8,10,12H2,1-2H3,(H,22,23,24)

InChI Key

NUTJUOHYJBWTSH-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidinecarboxylic acids. These are pyrimidines with a structure containing a carboxyl group attached to the pyrimidine ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Pyrimidinecarboxylic acids

Alternative Parents

Substituents

Pyrimidine-5-carboxylic acid
Phenoxy compound
Anisole
Methoxybenzene
Dialkylarylamine
Benzylamine
Phenol ether
Alkyl aryl ether
Aminopyrimidine
Chlorobenzene
Halobenzene
Aryl chloride
Aryl halide
Monocyclic benzene moiety
Imidolactam
Benzenoid
Heteroaromatic compound
Vinylogous amide
Pyrrolidine
Carboxylic acid ester
Ether
Carboxylic acid derivative
Azacycle
Organohalogen compound
Primary alcohol
Amine
Organic nitrogen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organochloride
Organonitrogen compound
Organooxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	3.12	ALOGPS
logP	3.86	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	14.98	ChemAxon
pKa (Strongest Basic)	5.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	96.81 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	113.76 m³·mol⁻¹	ChemAxon
Polarizability	44.52 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	195.256	30932474
DeepCCS	[M-H]-	192.543	30932474
DeepCCS	[M-2H]-	227.216	30932474
DeepCCS	[M+Na]+	202.417	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	13.4745 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.94 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2359.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	220.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	186.6 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	166.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	105.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	546.7 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	580.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	78.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1100.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	498.4 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1639.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	348.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	415.2 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	257.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	134.3 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	10.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate	CCOC(=O)C1=CN=C(N=C1NCC1=CC(Cl)=C(OC)C=C1)N1CCCC1CO	4668.8	Standard polar	33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate	CCOC(=O)C1=CN=C(N=C1NCC1=CC(Cl)=C(OC)C=C1)N1CCCC1CO	3435.3	Standard non polar	33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate	CCOC(=O)C1=CN=C(N=C1NCC1=CC(Cl)=C(OC)C=C1)N1CCCC1CO	3489.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate,2TMS,isomer #1	CCOC(=O)C1=CN=C(N2CCCC2CO[Si](C)(C)C)N=C1N(CC1=CC=C(OC)C(Cl)=C1)[Si](C)(C)C	3392.2	Semi standard non polar	33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate,2TMS,isomer #1	CCOC(=O)C1=CN=C(N2CCCC2CO[Si](C)(C)C)N=C1N(CC1=CC=C(OC)C(Cl)=C1)[Si](C)(C)C	3170.0	Standard non polar	33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate,2TMS,isomer #1	CCOC(=O)C1=CN=C(N2CCCC2CO[Si](C)(C)C)N=C1N(CC1=CC=C(OC)C(Cl)=C1)[Si](C)(C)C	4307.9	Standard polar	33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate,2TBDMS,isomer #1	CCOC(=O)C1=CN=C(N2CCCC2CO[Si](C)(C)C(C)(C)C)N=C1N(CC1=CC=C(OC)C(Cl)=C1)[Si](C)(C)C(C)(C)C	3688.2	Semi standard non polar	33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate,2TBDMS,isomer #1	CCOC(=O)C1=CN=C(N2CCCC2CO[Si](C)(C)C(C)(C)C)N=C1N(CC1=CC=C(OC)C(Cl)=C1)[Si](C)(C)C(C)(C)C	3585.5	Standard non polar	33892256
(S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate,2TBDMS,isomer #1	CCOC(=O)C1=CN=C(N2CCCC2CO[Si](C)(C)C(C)(C)C)N=C1N(CC1=CC=C(OC)C(Cl)=C1)[Si](C)(C)C(C)(C)C	4390.9	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate GC-MS (Non-derivatized) - 70eV, Positive	splash10-056s-3109000000-583a9b2605bc09129cee	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 10V, Positive-QTOF	splash10-00di-0103900000-a732388f735f3e165056	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 20V, Positive-QTOF	splash10-0a6r-0709200000-d3bae7f6be4e7c3bcfe0	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 40V, Positive-QTOF	splash10-056r-0903000000-425ca8eec6f3450f1660	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 10V, Negative-QTOF	splash10-014i-1014900000-c4743fea6488129dbaf0	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 20V, Negative-QTOF	splash10-015a-0149200000-fd0df7943899312f6566	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate 40V, Negative-QTOF	splash10-000x-6941000000-fc1e764005f368ccb315	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

11532233

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

22665593

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for (S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate (HMDB0246161)

MOL for HMDB0246161 ((S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate)

3D MOL for HMDB0246161 ((S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate)

3D SDF for HMDB0246161 ((S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate)

3D-SDF for HMDB0246161 ((S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate)

PDB for HMDB0246161 ((S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate)

3D PDB for HMDB0246161 ((S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate)

SMILES for HMDB0246161 ((S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate)

INCHI for HMDB0246161 ((S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate)

Structure for HMDB0246161 ((S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate)

3D Structure for HMDB0246161 ((S)-Ethyl 4-((3-chloro-4-methoxybenzyl)amino)-2-(2-(hydroxymethyl)pyrrolidin-1-yl)pyrimidine-5-carboxylate)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra