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Showing metabocard for Amethopterin (HMDB0248287)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 01:33:03 UTC
Update Date2021-09-26 22:58:29 UTC
HMDB IDHMDB0248287
Secondary Accession NumbersNone
Metabolite Identification
Common NameAmethopterin
DescriptionAmethopterin, also known as methotrexate or mexate, belongs to the class of organic compounds known as methylthio-s-triazines. These are aromatic compounds containing a 1,3,5-triazine ring that is substituted at the 2-position with a methylthio group. In humans, amethopterin is involved in the methotrexate action pathway. Amethopterin is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on Amethopterin. This compound has been identified in human blood as reported by (PMID: 31557052 ). Amethopterin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Amethopterin 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0248287 (Amethopterin)

  Mrv1533004241521582D          

 33 35  0  0  0  0            999 V2000
   -9.2881   -4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5737   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5737   -5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2881   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0026   -5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7171   -6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7171   -7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0026   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2881   -7.0125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0026   -8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7171   -8.6625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4315   -8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4315   -7.4250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1460   -8.6625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2881   -8.6625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8592   -4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8592   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -2.0625    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
  5  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
  4  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  7 13  1  0  0  0  0
 12 14  1  0  0  0  0
 10 15  1  0  0  0  0
  2 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 20  1  0  0  0  0
 20 21  2  0  0  0  0
 16 21  1  0  0  0  0
 19 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 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
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
 25 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
M  END
Download

3D MOL for HMDB0248287 (Amethopterin)

HMDB0248287
     RDKit          3D
Amethopterin
 55 57  0  0  0  0  0  0  0  0999 V2000
    2.6256   -1.6049   -0.1021 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411   -0.2937    0.1976 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7515    0.7127    0.9207 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1387    0.8813    0.5087 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6378    1.9117   -0.2381 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9622    1.9580   -0.5615 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.7917    1.0091   -0.1601 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1075    1.0629   -0.4895 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.9716    0.1070   -0.0929 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3623    0.1699   -0.4465 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.5030   -0.9135    0.6438 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.2106   -1.0197    0.9989 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7674   -2.1388    1.7785 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3185   -0.0504    0.6003 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0261   -0.0814    0.9071 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7000   -0.0940   -0.2054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2615   -0.1811    0.7744 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5962   -0.0623    0.4159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9894    0.1378   -0.8699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3941    0.2058   -1.2098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7244    0.6372   -2.3313 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3725   -0.2250   -0.2501 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8137   -0.1988   -0.5230 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5166    0.7386    0.3959 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9894    0.7507    0.1072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7057    1.7337    0.9965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0527    2.4330    1.7822 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0808    1.8529    0.9355 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2772   -1.5882   -0.3544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4931   -2.5257    0.0357 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5775   -2.0144   -0.5956 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0065    0.2260   -1.8508 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3493    0.1087   -1.5093 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5162   -1.8379    0.4748 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8761   -2.3937    0.0721 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8719   -1.6419   -1.1994 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2237    1.6971    0.7354 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6264    0.4874    2.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9284    2.6673   -0.5475 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0247   -0.4105    0.1495 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6800    0.7559   -1.2388 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0904   -3.1240    1.5467 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1307   -2.0278    2.5766 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0217   -0.3332    1.8042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3065   -0.1227    1.2102 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1166   -0.5829    0.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9418    0.0986   -1.5879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0776    1.7518    0.4211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4099    0.3724    1.4567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4551   -0.2356    0.4080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2360    0.9190   -0.9537 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5835    2.4077    0.2824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0240   -2.6557    0.0580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3183    0.3806   -2.8650 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0655    0.1831   -2.3109 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
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  2  0
  2 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 26 28  1  0
 23 29  1  0
 29 30  2  0
 29 31  1  0
 19 32  1  0
 32 33  2  0
 15  4  1  0
 33 16  1  0
 14  7  1  0
  1 34  1  0
  1 35  1  0
  1 36  1  0
  3 37  1  0
  3 38  1  0
  5 39  1  0
 10 40  1  0
 10 41  1  0
 13 42  1  0
 13 43  1  0
 17 44  1  0
 18 45  1  0
 22 46  1  0
 23 47  1  0
 24 48  1  0
 24 49  1  0
 25 50  1  0
 25 51  1  0
 28 52  1  0
 31 53  1  0
 32 54  1  0
 33 55  1  0
M  END
Download

3D SDF for HMDB0248287 (Amethopterin)

  Mrv1533004241521582D          

 33 35  0  0  0  0            999 V2000
   -9.2881   -4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5737   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5737   -5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2881   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0026   -5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7171   -6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7171   -7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0026   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2881   -7.0125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0026   -8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7171   -8.6625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4315   -8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4315   -7.4250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1460   -8.6625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2881   -8.6625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8592   -4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8592   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -2.0625    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
  5  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
  4  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  7 13  1  0  0  0  0
 12 14  1  0  0  0  0
 10 15  1  0  0  0  0
  2 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 20  1  0  0  0  0
 20 21  2  0  0  0  0
 16 21  1  0  0  0  0
 19 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 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
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
 25 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0248287

> <DATABASE_NAME>
hmdb

> <SMILES>
CN(CC1=CN=C2N=C(N)N=C(N)C2=N1)C1=CC=C(C=C1)C(=O)NC(CCC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)

> <INCHI_KEY>
FBOZXECLQNJBKD-UHFFFAOYSA-N

> <FORMULA>
C20H22N8O5

> <MOLECULAR_WEIGHT>
454.447

> <EXACT_MASS>
454.17131584

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
55

> <JCHEM_AVERAGE_POLARIZABILITY>
46.124259620969646

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(4-{[(2,4-diaminopteridin-6-yl)methyl](methyl)amino}phenyl)formamido]pentanedioic acid

> <ALOGPS_LOGP>
-0.91

> <JCHEM_LOGP>
-0.23645228652255187

> <ALOGPS_LOGS>
-3.42

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.1116524908147625

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.260834795187151

> <JCHEM_PKA_STRONGEST_BASIC>
1.7987846523802966

> <JCHEM_POLAR_SURFACE_AREA>
210.53999999999996

> <JCHEM_REFRACTIVITY>
119.21079999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.71e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methotrexate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0248287 (Amethopterin)

HMDB0248287
     RDKit          3D
Amethopterin
 55 57  0  0  0  0  0  0  0  0999 V2000
    2.6256   -1.6049   -0.1021 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411   -0.2937    0.1976 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7515    0.7127    0.9207 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1387    0.8813    0.5087 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6378    1.9117   -0.2381 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9622    1.9580   -0.5615 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.7917    1.0091   -0.1601 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1075    1.0629   -0.4895 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.9716    0.1070   -0.0929 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3623    0.1699   -0.4465 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.5030   -0.9135    0.6438 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.2106   -1.0197    0.9989 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7674   -2.1388    1.7785 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3185   -0.0504    0.6003 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0261   -0.0814    0.9071 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7000   -0.0940   -0.2054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2615   -0.1811    0.7744 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5962   -0.0623    0.4159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9894    0.1378   -0.8699 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3941    0.2058   -1.2098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7244    0.6372   -2.3313 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3725   -0.2250   -0.2501 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8137   -0.1988   -0.5230 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5166    0.7386    0.3959 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9894    0.7507    0.1072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7057    1.7337    0.9965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0527    2.4330    1.7822 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0808    1.8529    0.9355 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2772   -1.5882   -0.3544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4931   -2.5257    0.0357 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5775   -2.0144   -0.5956 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0065    0.2260   -1.8508 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3493    0.1087   -1.5093 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5162   -1.8379    0.4748 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8761   -2.3937    0.0721 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8719   -1.6419   -1.1994 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2237    1.6971    0.7354 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6264    0.4874    2.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9284    2.6673   -0.5475 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0247   -0.4105    0.1495 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6800    0.7559   -1.2388 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0904   -3.1240    1.5467 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1307   -2.0278    2.5766 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0217   -0.3332    1.8042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3065   -0.1227    1.2102 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1166   -0.5829    0.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9418    0.0986   -1.5879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0776    1.7518    0.4211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4099    0.3724    1.4567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4551   -0.2356    0.4080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2360    0.9190   -0.9537 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5835    2.4077    0.2824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0240   -2.6557    0.0580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3183    0.3806   -2.8650 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0655    0.1831   -2.3109 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
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  2  0
  2 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 26 28  1  0
 23 29  1  0
 29 30  2  0
 29 31  1  0
 19 32  1  0
 32 33  2  0
 15  4  1  0
 33 16  1  0
 14  7  1  0
  1 34  1  0
  1 35  1  0
  1 36  1  0
  3 37  1  0
  3 38  1  0
  5 39  1  0
 10 40  1  0
 10 41  1  0
 13 42  1  0
 13 43  1  0
 17 44  1  0
 18 45  1  0
 22 46  1  0
 23 47  1  0
 24 48  1  0
 24 49  1  0
 25 50  1  0
 25 51  1  0
 28 52  1  0
 31 53  1  0
 32 54  1  0
 33 55  1  0
M  END
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PDB for HMDB0248287 (Amethopterin)

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0     -17.338  -8.470   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0     -16.004  -9.240   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0     -16.004 -10.780   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -17.338 -11.550   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -18.672 -10.780   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0     -20.005 -11.550   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0     -20.005 -13.090   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -18.672 -13.860   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0     -17.338 -13.090   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0     -18.672 -15.400   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0     -20.005 -16.170   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0     -21.339 -15.400   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0     -21.339 -13.860   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0     -22.673 -16.170   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0     -17.338 -16.170   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0     -14.670  -8.470   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -14.670  -6.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0     -13.337  -6.160   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0     -12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0     -12.003  -8.470   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0     -13.337  -9.240   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0     -10.669  -6.160   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0     -10.669  -4.620   0.000  0.00  0.00           O+0
HETATM   24  N   UNK     0      -9.336  -6.930   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0      -8.002  -6.160   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -5.335  -6.160   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -2.667  -6.160   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -4.001  -8.470   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -6.668  -3.850   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -9.336  -3.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   16                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   13                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8    4                                                       
CONECT   10    8   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12    7                                                       
CONECT   14   12                                                            
CONECT   15   10                                                            
CONECT   16    2   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20   16                                                       
CONECT   22   19   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26   31                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   25   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END
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3D PDB for HMDB0248287 (Amethopterin)

COMPND    HMDB0248287
HETATM    1  C1  UNL     1       2.626  -1.605  -0.102  1.00  0.00           C  
HETATM    2  N1  UNL     1       2.041  -0.294   0.198  1.00  0.00           N  
HETATM    3  C2  UNL     1       2.752   0.713   0.921  1.00  0.00           C  
HETATM    4  C3  UNL     1       4.139   0.881   0.509  1.00  0.00           C  
HETATM    5  C4  UNL     1       4.638   1.912  -0.238  1.00  0.00           C  
HETATM    6  N2  UNL     1       5.962   1.958  -0.561  1.00  0.00           N  
HETATM    7  C5  UNL     1       6.792   1.009  -0.160  1.00  0.00           C  
HETATM    8  N3  UNL     1       8.108   1.063  -0.489  1.00  0.00           N  
HETATM    9  C6  UNL     1       8.972   0.107  -0.093  1.00  0.00           C  
HETATM   10  N4  UNL     1      10.362   0.170  -0.447  1.00  0.00           N  
HETATM   11  N5  UNL     1       8.503  -0.914   0.644  1.00  0.00           N  
HETATM   12  C7  UNL     1       7.211  -1.020   0.999  1.00  0.00           C  
HETATM   13  N6  UNL     1       6.767  -2.139   1.779  1.00  0.00           N  
HETATM   14  C8  UNL     1       6.318  -0.050   0.600  1.00  0.00           C  
HETATM   15  N7  UNL     1       5.026  -0.081   0.907  1.00  0.00           N  
HETATM   16  C9  UNL     1       0.700  -0.094  -0.205  1.00  0.00           C  
HETATM   17  C10 UNL     1      -0.261  -0.181   0.774  1.00  0.00           C  
HETATM   18  C11 UNL     1      -1.596  -0.062   0.416  1.00  0.00           C  
HETATM   19  C12 UNL     1      -1.989   0.138  -0.870  1.00  0.00           C  
HETATM   20  C13 UNL     1      -3.394   0.206  -1.210  1.00  0.00           C  
HETATM   21  O1  UNL     1      -3.724   0.637  -2.331  1.00  0.00           O  
HETATM   22  N8  UNL     1      -4.373  -0.225  -0.250  1.00  0.00           N  
HETATM   23  C14 UNL     1      -5.814  -0.199  -0.523  1.00  0.00           C  
HETATM   24  C15 UNL     1      -6.517   0.739   0.396  1.00  0.00           C  
HETATM   25  C16 UNL     1      -7.989   0.751   0.107  1.00  0.00           C  
HETATM   26  C17 UNL     1      -8.706   1.734   0.997  1.00  0.00           C  
HETATM   27  O2  UNL     1      -8.053   2.433   1.782  1.00  0.00           O  
HETATM   28  O3  UNL     1     -10.081   1.853   0.936  1.00  0.00           O  
HETATM   29  C18 UNL     1      -6.277  -1.588  -0.354  1.00  0.00           C  
HETATM   30  O4  UNL     1      -5.493  -2.526   0.036  1.00  0.00           O  
HETATM   31  O5  UNL     1      -7.577  -2.014  -0.596  1.00  0.00           O  
HETATM   32  C19 UNL     1      -1.006   0.226  -1.851  1.00  0.00           C  
HETATM   33  C20 UNL     1       0.349   0.109  -1.509  1.00  0.00           C  
HETATM   34  H1  UNL     1       3.516  -1.838   0.475  1.00  0.00           H  
HETATM   35  H2  UNL     1       1.876  -2.394   0.072  1.00  0.00           H  
HETATM   36  H3  UNL     1       2.872  -1.642  -1.199  1.00  0.00           H  
HETATM   37  H4  UNL     1       2.224   1.697   0.735  1.00  0.00           H  
HETATM   38  H5  UNL     1       2.626   0.487   2.006  1.00  0.00           H  
HETATM   39  H6  UNL     1       3.928   2.667  -0.548  1.00  0.00           H  
HETATM   40  H7  UNL     1      11.025  -0.410   0.150  1.00  0.00           H  
HETATM   41  H8  UNL     1      10.680   0.756  -1.239  1.00  0.00           H  
HETATM   42  H9  UNL     1       7.090  -3.124   1.547  1.00  0.00           H  
HETATM   43  H10 UNL     1       6.131  -2.028   2.577  1.00  0.00           H  
HETATM   44  H11 UNL     1       0.022  -0.333   1.804  1.00  0.00           H  
HETATM   45  H12 UNL     1      -2.306  -0.123   1.210  1.00  0.00           H  
HETATM   46  H13 UNL     1      -4.117  -0.583   0.683  1.00  0.00           H  
HETATM   47  H14 UNL     1      -5.942   0.099  -1.588  1.00  0.00           H  
HETATM   48  H15 UNL     1      -6.078   1.752   0.421  1.00  0.00           H  
HETATM   49  H16 UNL     1      -6.410   0.372   1.457  1.00  0.00           H  
HETATM   50  H17 UNL     1      -8.455  -0.236   0.408  1.00  0.00           H  
HETATM   51  H18 UNL     1      -8.236   0.919  -0.954  1.00  0.00           H  
HETATM   52  H19 UNL     1     -10.584   2.408   0.282  1.00  0.00           H  
HETATM   53  H20 UNL     1      -8.024  -2.656   0.058  1.00  0.00           H  
HETATM   54  H21 UNL     1      -1.318   0.381  -2.865  1.00  0.00           H  
HETATM   55  H22 UNL     1       1.065   0.183  -2.311  1.00  0.00           H  
CONECT    1    2   34   35   36
CONECT    2    3   16
CONECT    3    4   37   38
CONECT    4    5    5   15
CONECT    5    6   39
CONECT    6    7    7
CONECT    7    8   14
CONECT    8    9    9
CONECT    9   10   11
CONECT   10   40   41
CONECT   11   12   12
CONECT   12   13   14
CONECT   13   42   43
CONECT   14   15   15
CONECT   16   17   17   33
CONECT   17   18   44
CONECT   18   19   19   45
CONECT   19   20   32
CONECT   20   21   21   22
CONECT   22   23   46
CONECT   23   24   29   47
CONECT   24   25   48   49
CONECT   25   26   50   51
CONECT   26   27   27   28
CONECT   28   52
CONECT   29   30   30   31
CONECT   31   53
CONECT   32   33   33   54
CONECT   33   55
END
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SMILES for HMDB0248287 (Amethopterin)

CN(CC1=CN=C2N=C(N)N=C(N)C2=N1)C1=CC=C(C=C1)C(=O)NC(CCC(O)=O)C(O)=O
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INCHI for HMDB0248287 (Amethopterin)

InChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-[(4-{[(4-amino-2-imino-2,3-dihydropteridin-6-yl)methyl](methyl)amino}phenyl)formamido]pentanedioateHMDB
TCMDC-125858TCMDC-125488TCMDC-123832MethotrexateHMDB
TCMDC-125858TCMDC-125488TCMDC-123832Methotrexic acidHMDB
Dicesium salt methotrexateHMDB
Hydrate, methotrexateHMDB
MethotrexateHMDB
Methotrexate hydrateHMDB
Methotrexate sodiumHMDB
Methotrexate, (D)-isomerHMDB
Methotrexate, (DL)-isomerHMDB
Methotrexate, dicesium saltHMDB
Methotrexate, disodium saltHMDB
Methotrexate, sodium saltHMDB
MexateHMDB
Sodium, methotrexateHMDB
Chemical FormulaC20H22N8O5
Average Molecular Weight454.447
Monoisotopic Molecular Weight454.17131584
IUPAC Name2-[(4-{[(2,4-diaminopteridin-6-yl)methyl](methyl)amino}phenyl)formamido]pentanedioic acid
Traditional Namemethotrexate
CAS Registry NumberNot Available
SMILES
CN(CC1=CN=C2N=C(N)N=C(N)C2=N1)C1=CC=C(C=C1)C(=O)NC(CCC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)
InChI KeyFBOZXECLQNJBKD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as methylthio-s-triazines. These are aromatic compounds containing a 1,3,5-triazine ring that is substituted at the 2-position with a methylthio group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTriazines
Sub Class1,3,5-triazines
Direct ParentMethylthio-s-triazines
Alternative Parents
Substituents
  • Methylthio-s-triazine
  • 2,4-diamine-s-triazine
  • Alkyl-2-thio-s-triazine
  • Aryl thioether
  • Amino-1,3,5-triazine
  • Aminotriazine
  • Secondary aliphatic/aromatic amine
  • Alkylarylthioether
  • N-aliphatic s-triazine
  • Heteroaromatic compound
  • Azacycle
  • Sulfenyl compound
  • Thioether
  • Secondary amine
  • Amine
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID3969
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMethotrexate
METLIN IDNot Available
PubChem Compound4112
PDB IDNot Available
ChEBI IDNot Available
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. 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 ]