Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (2)transporters (2) Show 4 proteins XML

enzymes (2)transporters (2) Show 4 proteins

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:51 UTC

Update Date

2022-03-07 02:51:53 UTC

HMDB ID

HMDB0015164

Secondary Accession Numbers

HMDB15164

Metabolite Identification

Common Name

Topotecan

Description

Topotecan is only found in individuals that have used or taken this drug. It is an antineoplastic agent used to treat ovarian cancer. It works by inhibiting DNA topoisomerases, type I. [PubChem]Topotecan has the same mechanism of action as irinotecan and is believed to exert its cytotoxic effects during the S-phase of DNA synthesis. Topoisomerase I relieves torsional strain in DNA by inducing reversible single strand breaks. Topotecan binds to the topoisomerase I-DNA complex and prevents religation of these single strand breaks. This ternary complex interferes with the moving replication fork, which leads to the induction of replication arrest and lethal double-stranded breaks in DNA. As mammalian cells cannot efficiently repair these double strand breaks, the formation of this ternary complex eventually leads to apoptosis (programmed cell death).Topotecan mimics a DNA base pair and binds at the site of DNA cleavage by intercalating between the upstream (âˆ’1) and downstream (+1) base pairs. Intercalation displaces the downstream DNA, thus preventing religation of the cleaved strand. By specifically binding to the enzymeâ€“substrate complex, Topotecan acts as an uncompetitive inhibitor.

Structure

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

1030
  Mrv0541 02231215112D          

 31 35  0  0  1  0            999 V2000
    5.5924    3.9997    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7341    1.9917    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4360    2.7051    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0526    3.9798    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8154   -3.5845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1504    1.4677    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2044   -0.4301    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4712   -2.9335    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3300    2.7108    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5793    2.2927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8648    1.0552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5424    0.9174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8648    2.7051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8767    0.1685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6922    0.2536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5793    1.4677    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1504    2.2927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1549    2.7012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8516    3.5643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3366    3.5701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5165   -0.6060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0127   -1.3013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8622   -1.2128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6376   -2.1082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5589    1.9821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8161   -2.1842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3957   -1.9249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1543   -2.8325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0394   -2.7402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6499   -3.0096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9478   -3.6070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 19  1  0  0  0  0
  1 20  1  0  0  0  0
  9  2  1  1  0  0  0
  3 17  2  0  0  0  0
  4 20  2  0  0  0  0
  5 28  1  0  0  0  0
  6 11  1  0  0  0  0
  6 12  1  0  0  0  0
  6 17  1  0  0  0  0
  7 15  2  0  0  0  0
  7 23  1  0  0  0  0
  8 26  1  0  0  0  0
  8 30  1  0  0  0  0
  8 31  1  0  0  0  0
  9 10  1  0  0  0  0
  9 18  1  0  0  0  0
  9 20  1  0  0  0  0
 10 13  2  0  0  0  0
 10 16  1  0  0  0  0
 11 15  1  0  0  0  0
 11 16  2  0  0  0  0
 12 14  1  0  0  0  0
 13 17  1  0  0  0  0
 13 19  1  0  0  0  0
 14 15  1  0  0  0  0
 14 21  2  0  0  0  0
 18 25  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 23 27  1  0  0  0  0
 24 26  1  0  0  0  0
 24 28  2  0  0  0  0
 27 29  2  0  0  0  0
 28 29  1  0  0  0  0
M  END

HMDB0015164
     RDKit          3D
Topotecan
 54 58  0  0  0  0  0  0  0  0999 V2000
    6.7330   -0.2289   -1.7575 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2858   -0.0571   -1.3179 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2188   -0.4514    0.1329 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6242   -1.7802    0.2707 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1050    0.3628    0.9930 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8882    1.2396    0.5603 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0495    0.1253    2.3592 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9686   -0.5972    2.9501 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7491   -0.4209    2.0801 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8616   -0.3483    0.7085 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7574   -0.1876   -0.0991 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5047   -0.0986    0.5066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3913   -0.1684    1.8375 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4949   -0.3282    2.6302 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3348   -0.3882    3.8777 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0130   -0.0461    2.1567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7199    0.0992    0.8646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0658    0.2489    0.5474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4342    0.3633   -0.7707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8132    0.5199   -1.1196 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7029    0.5563    0.0520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0905    0.5610   -0.3306 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9224    0.9420    0.8413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4695   -0.8838   -0.5872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2097    0.6428   -2.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4741    0.8086   -2.8197 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1877    0.6016   -3.4176 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8851    0.4513   -3.0870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4980    0.3329   -1.7781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2033    0.1855   -1.4180 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2107    0.0690   -0.1451 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2646   -0.9464   -1.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7933   -0.5780   -2.8117 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2564    0.7534   -1.6914 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9897    0.9962   -1.4748 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7014   -0.7587   -1.9536 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9563   -2.3532    0.6793 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1976   -1.6678    3.0494 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8235   -0.1794    3.9574 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8230   -0.1284   -1.1787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3835   -0.9031    2.7549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1121    0.8574    2.7942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8121    0.2807    1.3123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4529    1.3915    0.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5905   -0.3627    0.6892 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0382    0.0327    1.4534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9176    1.1857    0.4179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4573    1.7478    1.4145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6011   -1.3088   -1.1067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6132   -1.4001    0.3585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3145   -0.8222   -1.2629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3443    0.9165   -2.5487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5378    0.6996   -4.4443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1193    0.4221   -3.8576 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  6
  3  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 13 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 22 24  1  0
 20 25  1  0
 25 26  1  0
 25 27  2  0
 27 28  1  0
 28 29  2  0
 29 30  1  0
 30 31  2  0
 10  3  1  0
 31 12  1  0
 14  9  1  0
 31 17  1  0
 29 19  1  0
  1 32  1  0
  1 33  1  0
  1 34  1  0
  2 35  1  0
  2 36  1  0
  4 37  1  0
  8 38  1  0
  8 39  1  0
 11 40  1  0
 16 41  1  0
 16 42  1  0
 18 43  1  0
 21 44  1  0
 21 45  1  0
 23 46  1  0
 23 47  1  0
 23 48  1  0
 24 49  1  0
 24 50  1  0
 24 51  1  0
 26 52  1  0
 27 53  1  0
 28 54  1  0
M  END

1030
  Mrv0541 02231215112D          

 31 35  0  0  1  0            999 V2000
    5.5924    3.9997    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7341    1.9917    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4360    2.7051    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0526    3.9798    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8154   -3.5845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1504    1.4677    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2044   -0.4301    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4712   -2.9335    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3300    2.7108    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5793    2.2927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8648    1.0552    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5424    0.9174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8648    2.7051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8767    0.1685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6922    0.2536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5793    1.4677    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1504    2.2927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1549    2.7012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8516    3.5643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3366    3.5701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5165   -0.6060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0127   -1.3013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8622   -1.2128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6376   -2.1082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5589    1.9821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8161   -2.1842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3957   -1.9249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1543   -2.8325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0394   -2.7402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6499   -3.0096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9478   -3.6070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 19  1  0  0  0  0
  1 20  1  0  0  0  0
  9  2  1  1  0  0  0
  3 17  2  0  0  0  0
  4 20  2  0  0  0  0
  5 28  1  0  0  0  0
  6 11  1  0  0  0  0
  6 12  1  0  0  0  0
  6 17  1  0  0  0  0
  7 15  2  0  0  0  0
  7 23  1  0  0  0  0
  8 26  1  0  0  0  0
  8 30  1  0  0  0  0
  8 31  1  0  0  0  0
  9 10  1  0  0  0  0
  9 18  1  0  0  0  0
  9 20  1  0  0  0  0
 10 13  2  0  0  0  0
 10 16  1  0  0  0  0
 11 15  1  0  0  0  0
 11 16  2  0  0  0  0
 12 14  1  0  0  0  0
 13 17  1  0  0  0  0
 13 19  1  0  0  0  0
 14 15  1  0  0  0  0
 14 21  2  0  0  0  0
 18 25  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 23 27  1  0  0  0  0
 24 26  1  0  0  0  0
 24 28  2  0  0  0  0
 27 29  2  0  0  0  0
 28 29  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0015164

> <DATABASE_NAME>
hmdb

> <SMILES>
CC[C@@]1(O)C(=O)OCC2=C1C=C1N(CC3=CC4=C(C=CC(O)=C4CN(C)C)N=C13)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C23H23N3O5/c1-4-23(30)16-8-18-20-12(9-26(18)21(28)15(16)11-31-22(23)29)7-13-14(10-25(2)3)19(27)6-5-17(13)24-20/h5-8,27,30H,4,9-11H2,1-3H3/t23-/m0/s1

> <INCHI_KEY>
UCFGDBYHRUNTLO-QHCPKHFHSA-N

> <FORMULA>
C23H23N3O5

> <MOLECULAR_WEIGHT>
421.4458

> <EXACT_MASS>
421.163770861

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
44.85931866430069

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(19S)-8-[(dimethylamino)methyl]-19-ethyl-7,19-dihydroxy-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2,4(9),5,7,10,15(20)-heptaene-14,18-dione

> <ALOGPS_LOGP>
1.84

> <JCHEM_LOGP>
-0.35709507722102324

> <ALOGPS_LOGS>
-2.69

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
11.71625075471723

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.003999445526812

> <JCHEM_PKA_STRONGEST_BASIC>
9.826297371129254

> <JCHEM_POLAR_SURFACE_AREA>
103.19999999999999

> <JCHEM_REFRACTIVITY>
115.0161

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.61e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
topotecan

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0015164
     RDKit          3D
Topotecan
 54 58  0  0  0  0  0  0  0  0999 V2000
    6.7330   -0.2289   -1.7575 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2858   -0.0571   -1.3179 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2188   -0.4514    0.1329 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6242   -1.7802    0.2707 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1050    0.3628    0.9930 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8882    1.2396    0.5603 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0495    0.1253    2.3592 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9686   -0.5972    2.9501 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7491   -0.4209    2.0801 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8616   -0.3483    0.7085 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7574   -0.1876   -0.0991 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5047   -0.0986    0.5066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3913   -0.1684    1.8375 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4949   -0.3282    2.6302 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3348   -0.3882    3.8777 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0130   -0.0461    2.1567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7199    0.0992    0.8646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0658    0.2489    0.5474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4342    0.3633   -0.7707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8132    0.5199   -1.1196 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7029    0.5563    0.0520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0905    0.5610   -0.3306 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9224    0.9420    0.8413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4695   -0.8838   -0.5872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2097    0.6428   -2.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4741    0.8086   -2.8197 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1877    0.6016   -3.4176 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8851    0.4513   -3.0870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4980    0.3329   -1.7781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2033    0.1855   -1.4180 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2107    0.0690   -0.1451 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2646   -0.9464   -1.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7933   -0.5780   -2.8117 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2564    0.7534   -1.6914 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9897    0.9962   -1.4748 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7014   -0.7587   -1.9536 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9563   -2.3532    0.6793 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1976   -1.6678    3.0494 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8235   -0.1794    3.9574 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8230   -0.1284   -1.1787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3835   -0.9031    2.7549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1121    0.8574    2.7942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8121    0.2807    1.3123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4529    1.3915    0.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5905   -0.3627    0.6892 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0382    0.0327    1.4534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9176    1.1857    0.4179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4573    1.7478    1.4145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6011   -1.3088   -1.1067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6132   -1.4001    0.3585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3145   -0.8222   -1.2629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3443    0.9165   -2.5487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5378    0.6996   -4.4443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1193    0.4221   -3.8576 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  6
  3  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 13 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 22 24  1  0
 20 25  1  0
 25 26  1  0
 25 27  2  0
 27 28  1  0
 28 29  2  0
 29 30  1  0
 30 31  2  0
 10  3  1  0
 31 12  1  0
 14  9  1  0
 31 17  1  0
 29 19  1  0
  1 32  1  0
  1 33  1  0
  1 34  1  0
  2 35  1  0
  2 36  1  0
  4 37  1  0
  8 38  1  0
  8 39  1  0
 11 40  1  0
 16 41  1  0
 16 42  1  0
 18 43  1  0
 21 44  1  0
 21 45  1  0
 23 46  1  0
 23 47  1  0
 23 48  1  0
 24 49  1  0
 24 50  1  0
 24 51  1  0
 26 52  1  0
 27 53  1  0
 28 54  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 1030                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      10.439   7.466   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      12.570   3.718   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       6.414   5.050   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      13.165   7.429   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       7.122  -6.691   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       7.748   2.740   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       9.715  -0.803   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       4.613  -5.476   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      11.816   5.060   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.415   4.280   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.081   1.970   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.612   1.713   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.081   5.050   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.236   0.315   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.759   0.473   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.415   2.740   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.748   4.280   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.356   5.042   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.056   6.653   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.828   6.664   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.564  -1.131   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.490  -2.429   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.076  -2.264   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.790  -3.935   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      14.110   3.700   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.257  -4.077   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.072  -3.593   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.755  -5.287   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.407  -5.115   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.080  -5.618   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.503  -6.733   0.000  0.00  0.00           C+0
CONECT    1   19   20                                                       
CONECT    2    9                                                            
CONECT    3   17                                                            
CONECT    4   20                                                            
CONECT    5   28                                                            
CONECT    6   11   12   17                                                  
CONECT    7   15   23                                                       
CONECT    8   26   30   31                                                  
CONECT    9    2   10   18   20                                             
CONECT   10    9   13   16                                                  
CONECT   11    6   15   16                                                  
CONECT   12    6   14                                                       
CONECT   13   10   17   19                                                  
CONECT   14   12   15   21                                                  
CONECT   15    7   11   14                                                  
CONECT   16   10   11                                                       
CONECT   17    3    6   13                                                  
CONECT   18    9   25                                                       
CONECT   19    1   13                                                       
CONECT   20    1    4    9                                                  
CONECT   21   14   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23    7   22   27                                                  
CONECT   24   22   26   28                                                  
CONECT   25   18                                                            
CONECT   26    8   24                                                       
CONECT   27   23   29                                                       
CONECT   28    5   24   29                                                  
CONECT   29   27   28                                                       
CONECT   30    8                                                            
CONECT   31    8                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   70    0
END

COMPND    HMDB0015164
HETATM    1  C1  UNL     1       6.733  -0.229  -1.758  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.286  -0.057  -1.318  1.00  0.00           C  
HETATM    3  C3  UNL     1       5.219  -0.451   0.133  1.00  0.00           C  
HETATM    4  O1  UNL     1       5.624  -1.780   0.271  1.00  0.00           O  
HETATM    5  C4  UNL     1       6.105   0.363   0.993  1.00  0.00           C  
HETATM    6  O2  UNL     1       6.888   1.240   0.560  1.00  0.00           O  
HETATM    7  O3  UNL     1       6.049   0.125   2.359  1.00  0.00           O  
HETATM    8  C5  UNL     1       4.969  -0.597   2.950  1.00  0.00           C  
HETATM    9  C6  UNL     1       3.749  -0.421   2.080  1.00  0.00           C  
HETATM   10  C7  UNL     1       3.862  -0.348   0.709  1.00  0.00           C  
HETATM   11  C8  UNL     1       2.757  -0.188  -0.099  1.00  0.00           C  
HETATM   12  C9  UNL     1       1.505  -0.099   0.507  1.00  0.00           C  
HETATM   13  N1  UNL     1       1.391  -0.168   1.837  1.00  0.00           N  
HETATM   14  C10 UNL     1       2.495  -0.328   2.630  1.00  0.00           C  
HETATM   15  O4  UNL     1       2.335  -0.388   3.878  1.00  0.00           O  
HETATM   16  C11 UNL     1      -0.013  -0.046   2.157  1.00  0.00           C  
HETATM   17  C12 UNL     1      -0.720   0.099   0.865  1.00  0.00           C  
HETATM   18  C13 UNL     1      -2.066   0.249   0.547  1.00  0.00           C  
HETATM   19  C14 UNL     1      -2.434   0.363  -0.771  1.00  0.00           C  
HETATM   20  C15 UNL     1      -3.813   0.520  -1.120  1.00  0.00           C  
HETATM   21  C16 UNL     1      -4.703   0.556   0.052  1.00  0.00           C  
HETATM   22  N2  UNL     1      -6.091   0.561  -0.331  1.00  0.00           N  
HETATM   23  C17 UNL     1      -6.922   0.942   0.841  1.00  0.00           C  
HETATM   24  C18 UNL     1      -6.469  -0.884  -0.587  1.00  0.00           C  
HETATM   25  C19 UNL     1      -4.210   0.643  -2.423  1.00  0.00           C  
HETATM   26  O5  UNL     1      -5.474   0.809  -2.820  1.00  0.00           O  
HETATM   27  C20 UNL     1      -3.188   0.602  -3.418  1.00  0.00           C  
HETATM   28  C21 UNL     1      -1.885   0.451  -3.087  1.00  0.00           C  
HETATM   29  C22 UNL     1      -1.498   0.333  -1.778  1.00  0.00           C  
HETATM   30  N3  UNL     1      -0.203   0.186  -1.418  1.00  0.00           N  
HETATM   31  C23 UNL     1       0.211   0.069  -0.145  1.00  0.00           C  
HETATM   32  H1  UNL     1       7.265  -0.946  -1.086  1.00  0.00           H  
HETATM   33  H2  UNL     1       6.793  -0.578  -2.812  1.00  0.00           H  
HETATM   34  H3  UNL     1       7.256   0.753  -1.691  1.00  0.00           H  
HETATM   35  H4  UNL     1       4.990   0.996  -1.475  1.00  0.00           H  
HETATM   36  H5  UNL     1       4.701  -0.759  -1.954  1.00  0.00           H  
HETATM   37  H6  UNL     1       4.956  -2.353   0.679  1.00  0.00           H  
HETATM   38  H7  UNL     1       5.198  -1.668   3.049  1.00  0.00           H  
HETATM   39  H8  UNL     1       4.823  -0.179   3.957  1.00  0.00           H  
HETATM   40  H9  UNL     1       2.823  -0.128  -1.179  1.00  0.00           H  
HETATM   41  H10 UNL     1      -0.383  -0.903   2.755  1.00  0.00           H  
HETATM   42  H11 UNL     1      -0.112   0.857   2.794  1.00  0.00           H  
HETATM   43  H12 UNL     1      -2.812   0.281   1.312  1.00  0.00           H  
HETATM   44  H13 UNL     1      -4.453   1.392   0.745  1.00  0.00           H  
HETATM   45  H14 UNL     1      -4.591  -0.363   0.689  1.00  0.00           H  
HETATM   46  H15 UNL     1      -7.038   0.033   1.453  1.00  0.00           H  
HETATM   47  H16 UNL     1      -7.918   1.186   0.418  1.00  0.00           H  
HETATM   48  H17 UNL     1      -6.457   1.748   1.415  1.00  0.00           H  
HETATM   49  H18 UNL     1      -5.601  -1.309  -1.107  1.00  0.00           H  
HETATM   50  H19 UNL     1      -6.613  -1.400   0.358  1.00  0.00           H  
HETATM   51  H20 UNL     1      -7.314  -0.822  -1.263  1.00  0.00           H  
HETATM   52  H21 UNL     1      -6.344   0.917  -2.549  1.00  0.00           H  
HETATM   53  H22 UNL     1      -3.538   0.700  -4.444  1.00  0.00           H  
HETATM   54  H23 UNL     1      -1.119   0.422  -3.858  1.00  0.00           H  
CONECT    1    2   32   33   34
CONECT    2    3   35   36
CONECT    3    4    5   10
CONECT    4   37
CONECT    5    6    6    7
CONECT    7    8
CONECT    8    9   38   39
CONECT    9   10   10   14
CONECT   10   11
CONECT   11   12   12   40
CONECT   12   13   31
CONECT   13   14   16
CONECT   14   15   15
CONECT   16   17   41   42
CONECT   17   18   18   31
CONECT   18   19   43
CONECT   19   20   20   29
CONECT   20   21   25
CONECT   21   22   44   45
CONECT   22   23   24
CONECT   23   46   47   48
CONECT   24   49   50   51
CONECT   25   26   27   27
CONECT   26   52
CONECT   27   28   53
CONECT   28   29   29   54
CONECT   29   30
CONECT   30   31   31
END

HMDB0015164
     RDKit          3D
Topotecan
 54 58  0  0  0  0  0  0  0  0999 V2000
    6.7330   -0.2289   -1.7575 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2858   -0.0571   -1.3179 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2188   -0.4514    0.1329 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6242   -1.7802    0.2707 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1050    0.3628    0.9930 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8882    1.2396    0.5603 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0495    0.1253    2.3592 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9686   -0.5972    2.9501 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7491   -0.4209    2.0801 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8616   -0.3483    0.7085 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7574   -0.1876   -0.0991 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5047   -0.0986    0.5066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3913   -0.1684    1.8375 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4949   -0.3282    2.6302 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3348   -0.3882    3.8777 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0130   -0.0461    2.1567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7199    0.0992    0.8646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0658    0.2489    0.5474 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4342    0.3633   -0.7707 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8132    0.5199   -1.1196 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7029    0.5563    0.0520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0905    0.5610   -0.3306 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9224    0.9420    0.8413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4695   -0.8838   -0.5872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2097    0.6428   -2.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4741    0.8086   -2.8197 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1877    0.6016   -3.4176 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8851    0.4513   -3.0870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4980    0.3329   -1.7781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2033    0.1855   -1.4180 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2107    0.0690   -0.1451 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2646   -0.9464   -1.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7933   -0.5780   -2.8117 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2564    0.7534   -1.6914 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9897    0.9962   -1.4748 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7014   -0.7587   -1.9536 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9563   -2.3532    0.6793 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1976   -1.6678    3.0494 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8235   -0.1794    3.9574 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8230   -0.1284   -1.1787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3835   -0.9031    2.7549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1121    0.8574    2.7942 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8121    0.2807    1.3123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4529    1.3915    0.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5905   -0.3627    0.6892 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0382    0.0327    1.4534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9176    1.1857    0.4179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4573    1.7478    1.4145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6011   -1.3088   -1.1067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6132   -1.4001    0.3585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3145   -0.8222   -1.2629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3443    0.9165   -2.5487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5378    0.6996   -4.4443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1193    0.4221   -3.8576 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  6
  3  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 13 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 22 24  1  0
 20 25  1  0
 25 26  1  0
 25 27  2  0
 27 28  1  0
 28 29  2  0
 29 30  1  0
 30 31  2  0
 10  3  1  0
 31 12  1  0
 14  9  1  0
 31 17  1  0
 29 19  1  0
  1 32  1  0
  1 33  1  0
  1 34  1  0
  2 35  1  0
  2 36  1  0
  4 37  1  0
  8 38  1  0
  8 39  1  0
 11 40  1  0
 16 41  1  0
 16 42  1  0
 18 43  1  0
 21 44  1  0
 21 45  1  0
 23 46  1  0
 23 47  1  0
 23 48  1  0
 24 49  1  0
 24 50  1  0
 24 51  1  0
 26 52  1  0
 27 53  1  0
 28 54  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
9-[(Dimethylamino)methyl]-10-hydroxy-(4S)-camptothecin	ChEBI
Topotecane	ChEBI
Topotecanum	ChEBI
Hycamtin	Kegg
Topotecan lactone	HMDB
SK And F 104864 a	HMDB
SK And F-104864-a	HMDB
SK And F104864a	HMDB
Topotecan hydrochloride	HMDB
9-Dimethylaminomethyl-10-hydroxycamptothecin	HMDB
Nogitecan hydrochloride	HMDB
SmithKline beecham brand OF topotecan hydrochloride	HMDB
Hycamtamine	HMDB
Hydrochloride, nogitecan	HMDB
Topotecan monohydrochloride, (S)-isomer	HMDB
9 Dimethylaminomethyl 10 hydroxycamptothecin	HMDB
Hydrochloride, topotecan	HMDB

Chemical Formula

C₂₃H₂₃N₃O₅

Average Molecular Weight

421.4458

Monoisotopic Molecular Weight

421.163770861

IUPAC Name

(19S)-8-[(dimethylamino)methyl]-19-ethyl-7,19-dihydroxy-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹¹.0⁴,⁹.0¹⁵,²⁰]henicosa-1(21),2,4(9),5,7,10,15(20)-heptaene-14,18-dione

Traditional Name

topotecan

CAS Registry Number

119413-54-6

SMILES

CC[C@@]1(O)C(=O)OCC2=C1C=C1N(CC3=CC4=C(C=CC(O)=C4CN(C)C)N=C13)C2=O

InChI Identifier

InChI=1S/C23H23N3O5/c1-4-23(30)16-8-18-20-12(9-26(18)21(28)15(16)11-31-22(23)29)7-13-14(10-25(2)3)19(27)6-5-17(13)24-20/h5-8,27,30H,4,9-11H2,1-3H3/t23-/m0/s1

InChI Key

UCFGDBYHRUNTLO-QHCPKHFHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as camptothecins. These are heterocyclic compounds comprising a planar pentacyclic ring structure, that includes a pyrrolo[3,4-beta]-quinoline moiety (rings A, B and C), conjugated pyridone moiety (ring D) and one chiral center at position 20 within the alpha-hydroxy lactone ring with (S) configuration (the E-ring).

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Camptothecins

Sub Class

Not Available

Direct Parent

Camptothecins

Alternative Parents

Substituents

Camptothecin
Hydroxyquinoline
Pyranopyridine
Quinoline
1-hydroxy-2-unsubstituted benzenoid
Pyridinone
Aralkylamine
Benzenoid
Pyridine
Heteroaromatic compound
Tertiary alcohol
Carboxylic acid ester
Amino acid or derivatives
Lactam
Tertiary aliphatic amine
Tertiary amine
Lactone
Oxacycle
Carboxylic acid derivative
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Organopnictogen compound
Alcohol
Organic oxide
Hydrocarbon derivative
Carbonyl group
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

pyranoindolizinoquinoline (CHEBI:63632 )

Ontology

Not Available

Urine (PMID: 21059682)

Non-excretory biofluid

Blood (PMID: 21059682)

Cellular substructure

Cytoplasm (HMDB: HMDB0015164)
Membrane (HMDB: HMDB0015164)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	213 - 218 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.86 g/L	Not Available
LogP	0.8	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.86 g/L	ALOGPS
logP	1.84	ALOGPS
logP	-0.36	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	8	ChemAxon
pKa (Strongest Basic)	9.83	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	103.2 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	115.02 m³·mol⁻¹	ChemAxon
Polarizability	44.86 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	196.06	31661259
DarkChem	[M-H]-	196.796	31661259
DeepCCS	[M-2H]-	226.836	30932474
DeepCCS	[M+Na]+	202.094	30932474
AllCCS	[M+H]+	199.0	32859911
AllCCS	[M+H-H2O]+	196.4	32859911
AllCCS	[M+NH4]+	201.4	32859911
AllCCS	[M+Na]+	202.1	32859911
AllCCS	[M-H]-	205.7	32859911
AllCCS	[M+Na-2H]-	206.1	32859911
AllCCS	[M+HCOO]-	206.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Topotecan	CC[C@@]1(O)C(=O)OCC2=C1C=C1N(CC3=CC4=C(C=CC(O)=C4CN(C)C)N=C13)C2=O	4501.8	Standard polar	33892256
Topotecan	CC[C@@]1(O)C(=O)OCC2=C1C=C1N(CC3=CC4=C(C=CC(O)=C4CN(C)C)N=C13)C2=O	3281.2	Standard non polar	33892256
Topotecan	CC[C@@]1(O)C(=O)OCC2=C1C=C1N(CC3=CC4=C(C=CC(O)=C4CN(C)C)N=C13)C2=O	4161.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Topotecan,1TMS,isomer #1	CC[C@@]1(O[Si](C)(C)C)C(=O)OCC2=C1C=C1C3=NC4=CC=C(O)C(CN(C)C)=C4C=C3CN1C2=O	3617.4	Semi standard non polar	33892256
Topotecan,1TMS,isomer #2	CC[C@@]1(O)C(=O)OCC2=C1C=C1C3=NC4=CC=C(O[Si](C)(C)C)C(CN(C)C)=C4C=C3CN1C2=O	3622.2	Semi standard non polar	33892256
Topotecan,2TMS,isomer #1	CC[C@@]1(O[Si](C)(C)C)C(=O)OCC2=C1C=C1C3=NC4=CC=C(O[Si](C)(C)C)C(CN(C)C)=C4C=C3CN1C2=O	3605.3	Semi standard non polar	33892256
Topotecan,1TBDMS,isomer #1	CC[C@@]1(O[Si](C)(C)C(C)(C)C)C(=O)OCC2=C1C=C1C3=NC4=CC=C(O)C(CN(C)C)=C4C=C3CN1C2=O	3810.2	Semi standard non polar	33892256
Topotecan,1TBDMS,isomer #2	CC[C@@]1(O)C(=O)OCC2=C1C=C1C3=NC4=CC=C(O[Si](C)(C)C(C)(C)C)C(CN(C)C)=C4C=C3CN1C2=O	3831.6	Semi standard non polar	33892256
Topotecan,2TBDMS,isomer #1	CC[C@@]1(O[Si](C)(C)C(C)(C)C)C(=O)OCC2=C1C=C1C3=NC4=CC=C(O[Si](C)(C)C(C)(C)C)C(CN(C)C)=C4C=C3CN1C2=O	3972.3	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Topotecan GC-MS (Non-derivatized) - 70eV, Positive	splash10-01rw-0019000000-dd5f6ac57d5951105684	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Topotecan GC-MS (2 TMS) - 70eV, Positive	splash10-0kmi-3001490000-ae90c2325c77269d874b	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Topotecan GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Topotecan GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Topotecan , positive-QTOF	splash10-00b9-0019400000-11f24a2a9b88f6c67514	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Topotecan 35V, Positive-QTOF	splash10-004i-1009000000-b9244ee1f6cd61fee4f2	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Topotecan 35V, Negative-QTOF	splash10-004i-0009000000-d66ee57d6e010d309c66	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Topotecan 10V, Positive-QTOF	splash10-00di-0006900000-89514722d3cccd3d4496	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Topotecan 20V, Positive-QTOF	splash10-00b9-0019300000-58bcf8842222fe631eca	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Topotecan 40V, Positive-QTOF	splash10-004i-1097000000-5b71ebf26d18a059bf0c	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Topotecan 10V, Negative-QTOF	splash10-00di-0004900000-c6c85b983396e6199196	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Topotecan 20V, Negative-QTOF	splash10-00fr-1009500000-740f8b3ec7e0bca5f75f	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Topotecan 40V, Negative-QTOF	splash10-0pwc-3029000000-65747933e72b20c9b71f	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Topotecan 10V, Positive-QTOF	splash10-00b9-0009500000-6c4802693f32d6eec744	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Topotecan 20V, Positive-QTOF	splash10-004i-0009000000-258882d388fa7db50bff	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Topotecan 40V, Positive-QTOF	splash10-05i3-4039100000-203d71abf98396934b86	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Topotecan 10V, Negative-QTOF	splash10-004i-0009100000-c19a7f2e40a8ab89986a	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Topotecan 20V, Negative-QTOF	splash10-004i-0009000000-a6970c65760ce14af472	2021-10-11	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Topotecan 40V, Negative-QTOF	splash10-01di-1029000000-30fc22abe375909eff46	2021-10-11	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-29	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB01030	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB01030	21059682	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB01030

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

54705

KEGG Compound ID

C11158

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Topotecan

METLIN ID

Not Available

PubChem Compound

60700

PDB ID

TTC

ChEBI ID

63632

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

Herben VM, ten Bokkel Huinink WW, Beijnen JH: Clinical pharmacokinetics of topotecan. Clin Pharmacokinet. 1996 Aug;31(2):85-102. [PubMed:8853931 ]
Dennis MJ, Beijnen JH, Grochow LB, van Warmerdam LJ: An overview of the clinical pharmacology of topotecan. Semin Oncol. 1997 Feb;24(1 Suppl 5):S5-12-S5-18. [PubMed:9122737 ]
Kollmannsberger C, Mross K, Jakob A, Kanz L, Bokemeyer C: Topotecan - A novel topoisomerase I inhibitor: pharmacology and clinical experience. Oncology. 1999;56(1):1-12. [PubMed:9885371 ]

Enzymes

Enzyme Details

1. Cytochrome P450 3A4

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
Gene Name:: CYP3A4
Uniprot ID:: P08684
Molecular weight:: 57255.585

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Enzyme Details

2. DNA topoisomerase I, mitochondrial

General function:: Involved in DNA binding
Specific function:: Relieves DNA strain that arise during duplication of mitochondrial DNA
Gene Name:: TOP1MT
Uniprot ID:: Q969P6
Molecular weight:: 69871.4

References

Kosovsky MJ, Soslau G: Immunological identification of human platelet mitochondrial DNA topoisomerase I. Biochim Biophys Acta. 1993 Jun 24;1164(1):101-7. [PubMed:8390858 ]

Transporters

Enzyme Details

1. Multidrug resistance protein 1

General function:: Involved in ATP binding
Specific function:: Energy-dependent efflux pump responsible for decreased drug accumulation in multidrug-resistant cells
Gene Name:: ABCB1
Uniprot ID:: P08183
Molecular weight:: 141477.3

References

Collett A, Tanianis-Hughes J, Hallifax D, Warhurst G: Predicting P-glycoprotein effects on oral absorption: correlation of transport in Caco-2 with drug pharmacokinetics in wild-type and mdr1a(-/-) mice in vivo. Pharm Res. 2004 May;21(5):819-26. [PubMed:15180340 ]
Carcaboso AM, Elmeliegy MA, Shen J, Juel SJ, Zhang ZM, Calabrese C, Tracey L, Waters CM, Stewart CF: Tyrosine kinase inhibitor gefitinib enhances topotecan penetration of gliomas. Cancer Res. 2010 Jun 1;70(11):4499-508. doi: 10.1158/0008-5472.CAN-09-4264. Epub 2010 May 11. [PubMed:20460504 ]
Shen J, Carcaboso AM, Hubbard KE, Tagen M, Wynn HG, Panetta JC, Waters CM, Elmeliegy MA, Stewart CF: Compartment-specific roles of ATP-binding cassette transporters define differential topotecan distribution in brain parenchyma and cerebrospinal fluid. Cancer Res. 2009 Jul 15;69(14):5885-92. doi: 10.1158/0008-5472.CAN-09-0700. Epub 2009 Jun 30. [PubMed:19567673 ]

Enzyme Details

2. ATP-binding cassette sub-family G member 2

General function:: Involved in ATP binding
Specific function:: Xenobiotic transporter that may play an important role in the exclusion of xenobiotics from the brain. May be involved in brain-to-blood efflux. Appears to play a major role in the multidrug resistance phenotype of several cancer cell lines. When overexpressed, the transfected cells become resistant to mitoxantrone, daunorubicin and doxorubicin, display diminished intracellular accumulation of daunorubicin, and manifest an ATP- dependent increase in the efflux of rhodamine 123
Gene Name:: ABCG2
Uniprot ID:: Q9UNQ0
Molecular weight:: 72313.5

References

Houghton PJ, Germain GS, Harwood FC, Schuetz JD, Stewart CF, Buchdunger E, Traxler P: Imatinib mesylate is a potent inhibitor of the ABCG2 (BCRP) transporter and reverses resistance to topotecan and SN-38 in vitro. Cancer Res. 2004 Apr 1;64(7):2333-7. [PubMed:15059881 ]
Maliepaard M, van Gastelen MA, Tohgo A, Hausheer FH, van Waardenburg RC, de Jong LA, Pluim D, Beijnen JH, Schellens JH: Circumvention of breast cancer resistance protein (BCRP)-mediated resistance to camptothecins in vitro using non-substrate drugs or the BCRP inhibitor GF120918. Clin Cancer Res. 2001 Apr;7(4):935-41. [PubMed:11309344 ]
Sugimoto Y, Tsukahara S, Imai Y, Sugimoto Y, Ueda K, Tsuruo T: Reversal of breast cancer resistance protein-mediated drug resistance by estrogen antagonists and agonists. Mol Cancer Ther. 2003 Jan;2(1):105-12. [PubMed:12533678 ]
Maliepaard M, van Gastelen MA, de Jong LA, Pluim D, van Waardenburg RC, Ruevekamp-Helmers MC, Floot BG, Schellens JH: Overexpression of the BCRP/MXR/ABCP gene in a topotecan-selected ovarian tumor cell line. Cancer Res. 1999 Sep 15;59(18):4559-63. [PubMed:10493507 ]
Jonker JW, Smit JW, Brinkhuis RF, Maliepaard M, Beijnen JH, Schellens JH, Schinkel AH: Role of breast cancer resistance protein in the bioavailability and fetal penetration of topotecan. J Natl Cancer Inst. 2000 Oct 18;92(20):1651-6. [PubMed:11036110 ]
Allen JD, Van Dort SC, Buitelaar M, van Tellingen O, Schinkel AH: Mouse breast cancer resistance protein (Bcrp1/Abcg2) mediates etoposide resistance and transport, but etoposide oral availability is limited primarily by P-glycoprotein. Cancer Res. 2003 Mar 15;63(6):1339-44. [PubMed:12649196 ]
Breedveld P, Zelcer N, Pluim D, Sonmezer O, Tibben MM, Beijnen JH, Schinkel AH, van Tellingen O, Borst P, Schellens JH: Mechanism of the pharmacokinetic interaction between methotrexate and benzimidazoles: potential role for breast cancer resistance protein in clinical drug-drug interactions. Cancer Res. 2004 Aug 15;64(16):5804-11. [PubMed:15313923 ]
Carcaboso AM, Elmeliegy MA, Shen J, Juel SJ, Zhang ZM, Calabrese C, Tracey L, Waters CM, Stewart CF: Tyrosine kinase inhibitor gefitinib enhances topotecan penetration of gliomas. Cancer Res. 2010 Jun 1;70(11):4499-508. doi: 10.1158/0008-5472.CAN-09-4264. Epub 2010 May 11. [PubMed:20460504 ]
Shen J, Carcaboso AM, Hubbard KE, Tagen M, Wynn HG, Panetta JC, Waters CM, Elmeliegy MA, Stewart CF: Compartment-specific roles of ATP-binding cassette transporters define differential topotecan distribution in brain parenchyma and cerebrospinal fluid. Cancer Res. 2009 Jul 15;69(14):5885-92. doi: 10.1158/0008-5472.CAN-09-0700. Epub 2009 Jun 30. [PubMed:19567673 ]
Rocchi E, Khodjakov A, Volk EL, Yang CH, Litman T, Bates SE, Schneider E: The product of the ABC half-transporter gene ABCG2 (BCRP/MXR/ABCP) is expressed in the plasma membrane. Biochem Biophys Res Commun. 2000 Apr 29;271(1):42-6. [PubMed:10777678 ]
Ishii M, Iwahana M, Mitsui I, Minami M, Imagawa S, Tohgo A, Ejima A: Growth inhibitory effect of a new camptothecin analog, DX-8951f, on various drug-resistant sublines including BCRP-mediated camptothecin derivative-resistant variants derived from the human lung cancer cell line PC-6. Anticancer Drugs. 2000 Jun;11(5):353-62. [PubMed:10912951 ]
Yang CH, Schneider E, Kuo ML, Volk EL, Rocchi E, Chen YC: BCRP/MXR/ABCP expression in topotecan-resistant human breast carcinoma cells. Biochem Pharmacol. 2000 Sep 15;60(6):831-7. [PubMed:10930538 ]

Showing metabocard for Topotecan (HMDB0015164)

MOL for HMDB0015164 (Topotecan)

3D MOL for HMDB0015164 (Topotecan)

3D SDF for HMDB0015164 (Topotecan)

3D-SDF for HMDB0015164 (Topotecan)

PDB for HMDB0015164 (Topotecan)

3D PDB for HMDB0015164 (Topotecan)

SMILES for HMDB0015164 (Topotecan)

INCHI for HMDB0015164 (Topotecan)

Structure for HMDB0015164 (Topotecan)

3D Structure for HMDB0015164 (Topotecan)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

References

References

Transporters

References

References