data_DM2
#
_chem_comp.id DM2
_chem_comp.name DOXORUBICIN
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAD
_chem_comp.formula "C27 H29 N O11"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ADRIAMYCIN
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2021-03-01
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 543.519
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DM2
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 151D
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
DM2 C1 C1 C 0 1 Y N N N N N 15.226 18.450 4.896 -0.791 -0.376 6.114 C1 DM2 1
DM2 C2 C2 C 0 1 Y N N N N N 16.429 19.161 4.909 0.106 0.151 7.027 C2 DM2 2
DM2 C3 C3 C 0 1 Y N N N N N 17.654 18.469 4.880 1.331 0.630 6.611 C3 DM2 3
DM2 C4 C4 C 0 1 Y N N N N N 17.677 17.063 4.829 1.682 0.590 5.264 C4 DM2 4
DM2 O4 O4 O 0 1 N N N N N N 18.898 16.388 4.808 2.887 1.062 4.859 O4 DM2 5
DM2 C5 C5 C 0 1 Y N N N N N 16.456 16.353 4.816 0.784 0.066 4.332 C5 DM2 6
DM2 C6 C6 C 0 1 N N N N N N 16.409 14.946 4.803 1.136 0.008 2.900 C6 DM2 7
DM2 O6 O6 O 0 1 N N N N N N 17.561 14.211 4.771 2.284 0.186 2.539 O6 DM2 8
DM2 C7 C7 C 0 1 Y N N N N N 15.196 14.209 4.817 0.076 -0.262 1.910 C7 DM2 9
DM2 C8 C8 C 0 1 Y N N N N N 15.164 12.808 4.784 0.293 -0.040 0.553 C8 DM2 10
DM2 O8 O8 O 0 1 N N N N N N 16.295 12.032 4.788 1.493 0.428 0.131 O8 DM2 11
DM2 C9 C9 C 0 1 Y N N N N N 13.929 12.131 4.758 -0.721 -0.297 -0.379 C9 DM2 12
DM2 C10 C10 C 0 1 N N S N N N 13.995 10.639 4.786 -0.413 -0.024 -1.829 C10 DM2 13
DM2 O10 O10 O 0 1 N N N N N N 14.592 10.397 6.123 0.906 -0.487 -2.124 O10 DM2 14
DM2 C11 C11 C 0 1 N N N N N N 12.711 9.868 4.523 -1.412 -0.739 -2.736 C11 DM2 15
DM2 C12 C12 C 0 1 N N S N N N 11.569 10.600 5.359 -2.828 -0.395 -2.259 C12 DM2 16
DM2 O12 O12 O 0 1 N N N N N N 11.611 10.753 6.835 -3.784 -0.864 -3.212 O12 DM2 17
DM2 C13 C13 C 0 1 N N N N N N 10.269 9.864 5.071 -2.962 1.096 -2.096 C13 DM2 18
DM2 O13 O13 O 0 1 N N N N N N 9.543 10.187 3.954 -2.780 1.605 -1.016 O13 DM2 19
DM2 C14 C14 C 0 1 N N N N N N 9.825 8.804 6.033 -3.323 1.954 -3.282 C14 DM2 20
DM2 O14 O14 O 0 1 N N N N N N 8.617 8.191 5.670 -3.389 3.323 -2.877 O14 DM2 21
DM2 C15 C15 C 0 1 N N N N N N 11.432 12.065 4.766 -3.061 -1.082 -0.915 C15 DM2 22
DM2 C16 C16 C 0 1 Y N N N N N 12.729 12.807 4.799 -1.936 -0.777 0.039 C16 DM2 23
DM2 C17 C17 C 0 1 Y N N N N N 12.761 14.224 4.827 -2.170 -1.005 1.402 C17 DM2 24
DM2 O17 O17 O 0 1 N N N N N N 11.570 14.889 4.797 -3.374 -1.478 1.809 O17 DM2 25
DM2 C18 C18 C 0 1 Y N N N N N 13.985 14.924 4.822 -1.174 -0.751 2.341 C18 DM2 26
DM2 C19 C19 C 0 1 N N N N N N 14.007 16.349 4.853 -1.410 -0.985 3.778 C19 DM2 27
DM2 O19 O19 O 0 1 N N N N N N 12.853 16.988 4.878 -2.373 -1.630 4.146 O19 DM2 28
DM2 C20 C20 C 0 1 Y N N N N N 15.244 17.040 4.865 -0.462 -0.426 4.765 C20 DM2 29
DM2 C21 C21 C 0 1 N N N N N N 20.164 17.131 4.894 3.562 1.529 6.029 C21 DM2 30
DM2 "C1'" C1* C 0 1 N N R N N N 15.508 9.325 6.325 1.598 0.601 -2.737 "C1'" DM2 31
DM2 "C2'" C2* C 0 1 N N N N N N 16.662 9.744 7.308 3.094 0.283 -2.798 "C2'" DM2 32
DM2 "C3'" C3* C 0 1 N N S N N N 15.986 9.896 8.700 3.298 -1.006 -3.599 "C3'" DM2 33
DM2 "N3'" N3* N 0 1 N N N N N N 17.069 10.218 9.702 4.735 -1.242 -3.796 "N3'" DM2 34
DM2 "C4'" C4* C 0 1 N N S N N N 15.236 8.613 9.132 2.607 -0.854 -4.959 "C4'" DM2 35
DM2 "O4'" O4* O 0 1 N N N N N N 16.324 7.597 9.201 3.273 0.154 -5.723 "O4'" DM2 36
DM2 "C5'" C5* C 0 1 N N S N N N 14.150 8.254 8.082 1.148 -0.450 -4.735 "C5'" DM2 37
DM2 "O5'" O5* O 0 1 N N N N N N 14.828 8.116 6.752 1.094 0.801 -4.056 "O5'" DM2 38
DM2 "C6'" C6* C 0 1 N N N N N N 13.470 6.895 8.316 0.441 -0.326 -6.086 "C6'" DM2 39
DM2 H1 H1 H 0 1 N N N N N N 14.268 18.998 4.910 -1.747 -0.749 6.450 H1 DM2 40
DM2 H2 H2 H 0 1 N N N N N N 16.411 20.263 4.942 -0.154 0.188 8.075 H2 DM2 41
DM2 H3 H3 H 0 1 N N N N N N 18.602 19.032 4.897 2.022 1.038 7.334 H3 DM2 42
DM2 HO8 HO8 H 0 1 N N N N N N 16.273 11.082 4.765 1.418 1.392 0.091 HO8 DM2 43
DM2 H10 H10 H 0 1 N N N N N N 14.584 10.240 3.927 -0.466 1.048 -2.011 H10 DM2 44
DM2 H111 1H11 H 0 0 N N N N N N 12.469 9.766 3.439 -1.256 -1.816 -2.677 H111 DM2 45
DM2 H112 2H11 H 0 0 N N N N N N 12.794 8.779 4.747 -1.279 -0.403 -3.764 H112 DM2 46
DM2 HO12 2HO1 H 0 0 N N N N N N 10.930 11.189 7.333 -4.658 -0.643 -2.862 HO12 DM2 47
DM2 H141 1H14 H 0 0 N N N N N N 10.626 8.042 6.178 -2.564 1.840 -4.057 H141 DM2 48
DM2 H142 2H14 H 0 0 N N N N N N 9.765 9.211 7.069 -4.291 1.643 -3.674 H142 DM2 49
DM2 HO14 4HO1 H 0 0 N N N N N N 8.335 7.519 6.279 -3.622 3.836 -3.663 HO14 DM2 50
DM2 H151 1H15 H 0 0 N N N N N N 11.003 12.046 3.737 -3.120 -2.160 -1.068 H151 DM2 51
DM2 H152 2H15 H 0 0 N N N N N N 10.625 12.636 5.282 -4.000 -0.729 -0.489 H152 DM2 52
DM2 HO17 7HO1 H 0 0 N N N N N N 11.591 15.838 4.815 -3.932 -0.707 1.985 HO17 DM2 53
DM2 H211 1H21 H 0 0 N N N N N N 21.139 16.591 4.877 4.541 1.920 5.752 H211 DM2 54
DM2 H212 2H21 H 0 0 N N N N N N 20.174 17.897 4.084 2.975 2.319 6.497 H212 DM2 55
DM2 H213 3H21 H 0 0 N N N N N N 20.133 17.768 5.808 3.686 0.704 6.731 H213 DM2 56
DM2 "H1'" H1* H 0 1 N N N N N N 15.984 9.090 5.344 1.444 1.506 -2.149 "H1'" DM2 57
DM2 "H2'1" 1H2* H 0 0 N N N N N N 17.530 9.044 7.305 3.621 1.103 -3.286 "H2'1" DM2 58
DM2 "H2'2" 2H2* H 0 0 N N N N N N 17.223 10.650 6.980 3.480 0.150 -1.787 "H2'2" DM2 59
DM2 "H3'" H3* H 0 1 N N N N N N 15.225 10.709 8.646 2.860 -1.846 -3.059 "H3'" DM2 60
DM2 "HN'1" 1HN* H 0 0 N N N N N N 16.625 10.317 10.615 5.144 -1.323 -2.877 "HN'1" DM2 61
DM2 "HN'2" 2HN* H 0 0 N N N N N N 17.623 11.032 9.439 4.823 -2.147 -4.233 "HN'2" DM2 62
DM2 "H4'" H4* H 0 1 N N N N N N 14.688 8.702 10.098 2.645 -1.802 -5.496 "H4'" DM2 63
DM2 "HO4'" *HO4 H 0 0 N N N N N N 15.863 6.809 9.466 2.807 0.217 -6.568 "HO4'" DM2 64
DM2 "H5'" H5* H 0 1 N N N N N N 13.382 9.060 8.145 0.650 -1.210 -4.134 "H5'" DM2 65
DM2 "H6'1" 1H6* H 0 0 N N N N N N 12.690 6.637 7.562 -0.597 -0.038 -5.927 "H6'1" DM2 66
DM2 "H6'2" 2H6* H 0 0 N N N N N N 14.232 6.083 8.381 0.940 0.432 -6.689 "H6'2" DM2 67
DM2 "H6'3" 3H6* H 0 0 N N N N N N 13.048 6.842 9.346 0.478 -1.284 -6.605 "H6'3" DM2 68
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
DM2 C1 C2 DOUB Y N 1
DM2 C1 C20 SING Y N 2
DM2 C1 H1 SING N N 3
DM2 C2 C3 SING Y N 4
DM2 C2 H2 SING N N 5
DM2 C3 C4 DOUB Y N 6
DM2 C3 H3 SING N N 7
DM2 C4 O4 SING N N 8
DM2 C4 C5 SING Y N 9
DM2 O4 C21 SING N N 10
DM2 C5 C6 SING N N 11
DM2 C5 C20 DOUB Y N 12
DM2 C6 O6 DOUB N N 13
DM2 C6 C7 SING N N 14
DM2 C7 C8 DOUB Y N 15
DM2 C7 C18 SING Y N 16
DM2 C8 O8 SING N N 17
DM2 C8 C9 SING Y N 18
DM2 O8 HO8 SING N N 19
DM2 C9 C10 SING N N 20
DM2 C9 C16 DOUB Y N 21
DM2 C10 O10 SING N N 22
DM2 C10 C11 SING N N 23
DM2 C10 H10 SING N N 24
DM2 O10 "C1'" SING N N 25
DM2 C11 C12 SING N N 26
DM2 C11 H111 SING N N 27
DM2 C11 H112 SING N N 28
DM2 C12 O12 SING N N 29
DM2 C12 C13 SING N N 30
DM2 C12 C15 SING N N 31
DM2 O12 HO12 SING N N 32
DM2 C13 O13 DOUB N N 33
DM2 C13 C14 SING N N 34
DM2 C14 O14 SING N N 35
DM2 C14 H141 SING N N 36
DM2 C14 H142 SING N N 37
DM2 O14 HO14 SING N N 38
DM2 C15 C16 SING N N 39
DM2 C15 H151 SING N N 40
DM2 C15 H152 SING N N 41
DM2 C16 C17 SING Y N 42
DM2 C17 O17 SING N N 43
DM2 C17 C18 DOUB Y N 44
DM2 O17 HO17 SING N N 45
DM2 C18 C19 SING N N 46
DM2 C19 O19 DOUB N N 47
DM2 C19 C20 SING N N 48
DM2 C21 H211 SING N N 49
DM2 C21 H212 SING N N 50
DM2 C21 H213 SING N N 51
DM2 "C1'" "C2'" SING N N 52
DM2 "C1'" "O5'" SING N N 53
DM2 "C1'" "H1'" SING N N 54
DM2 "C2'" "C3'" SING N N 55
DM2 "C2'" "H2'1" SING N N 56
DM2 "C2'" "H2'2" SING N N 57
DM2 "C3'" "N3'" SING N N 58
DM2 "C3'" "C4'" SING N N 59
DM2 "C3'" "H3'" SING N N 60
DM2 "N3'" "HN'1" SING N N 61
DM2 "N3'" "HN'2" SING N N 62
DM2 "C4'" "O4'" SING N N 63
DM2 "C4'" "C5'" SING N N 64
DM2 "C4'" "H4'" SING N N 65
DM2 "O4'" "HO4'" SING N N 66
DM2 "C5'" "O5'" SING N N 67
DM2 "C5'" "C6'" SING N N 68
DM2 "C5'" "H5'" SING N N 69
DM2 "C6'" "H6'1" SING N N 70
DM2 "C6'" "H6'2" SING N N 71
DM2 "C6'" "H6'3" SING N N 72
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
DM2 SMILES ACDLabs 10.04 O=C2c1c(O)c5c(c(O)c1C(=O)c3cccc(OC)c23)CC(O)(C(=O)CO)CC5OC4OC(C(O)C(N)C4)C
DM2 SMILES_CANONICAL CACTVS 3.341 COc1cccc2C(=O)c3c(O)c4C[C@](O)(C[C@H](O[C@H]5C[C@H](N)[C@H](O)[C@H](C)O5)c4c(O)c3C(=O)c12)C(=O)CO
DM2 SMILES CACTVS 3.341 COc1cccc2C(=O)c3c(O)c4C[C](O)(C[CH](O[CH]5C[CH](N)[CH](O)[CH](C)O5)c4c(O)c3C(=O)c12)C(=O)CO
DM2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@H]1[C@H]([C@H](C[C@@H](O1)O[C@H]2C[C@@](Cc3c2c(c4c(c3O)C(=O)c5cccc(c5C4=O)OC)O)(C(=O)CO)O)N)O
DM2 SMILES "OpenEye OEToolkits" 1.5.0 CC1C(C(CC(O1)OC2CC(Cc3c2c(c4c(c3O)C(=O)c5cccc(c5C4=O)OC)O)(C(=O)CO)O)N)O
DM2 InChI InChI 1.03 InChI=1S/C27H29NO11/c1-10-22(31)13(28)6-17(38-10)39-15-8-27(36,16(30)9-29)7-12-19(15)26(35)21-20(24(12)33)23(32)11-4-3-5-14(37-2)18(11)25(21)34/h3-5,10,13,15,17,22,29,31,33,35-36H,6-9,28H2,1-2H3/t10-,13-,15-,17-,22+,27-/m0/s1
DM2 InChIKey InChI 1.03 AOJJSUZBOXZQNB-TZSSRYMLSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
DM2 "SYSTEMATIC NAME" ACDLabs 10.04 "(1S,3S)-3,5,12-trihydroxy-3-(hydroxyacetyl)-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside"
DM2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (7S,9S)-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl-oxan-2-yl]oxy-6,9,11-trihydroxy-9-(2-hydroxyethanoyl)-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
DM2 'Create component' 1999-07-08 RCSB
DM2 'Modify descriptor' 2011-06-04 RCSB
DM2 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id DM2
_pdbx_chem_comp_synonyms.name ADRIAMYCIN
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id DM2
_pdbe_chem_comp_drugbank_details.drugbank_id DB00997
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Doxorubicin
_pdbe_chem_comp_drugbank_details.description
"Doxorubicin is a cytotoxic anthracycline antibiotic isolated from cultures of Streptomyces peucetius var. caesius along side with daunorubicin, another cytotoxic agent, in 1970.[A1575,A257709,A257614] Although they both have aglyconic and sugar moieties, doxorubicin's side chain terminates with a primary alcohol group compared to the methyl group of daunorubicin.[A257709] Although its detailed molecular mechanisms have yet to be understood, doxorubicin is generally thought to exert its effect through DNA intercalation, which eventually leads to DNA damage and the generation of reactive oxygen species.[A257614] Thanks to its efficacy and broad effect, doxorubicin was approved by the FDA in 1974 to treat a variety of cancer, including but not limited to breast, lung, gastric, ovarian, thyroid, non-Hodgkin’s and Hodgkin’s lymphoma, multiple myeloma, sarcoma, and pediatric cancers.[A1573,A257614,L45231] However, one of the major side effects of doxorubicin is cardiotoxicity, which excludes patients with poor heart function and requires treatment termination once the maximally tolerated cumulative dose is reached.[A257719]"
_pdbe_chem_comp_drugbank_details.cas_number 23214-92-8
_pdbe_chem_comp_drugbank_details.mechanism_of_action
"Generally, doxorubicin is thought to exert its antineoplastic activity through 2 primary mechanisms: intercalation into DNA and disrupt topoisomerase-mediated repairs and free radicals-mediated cellular damages.[A257614]  Doxorubicin can intercalate into DNA through the anthraquinone ring, which stabilizes the complex by forming hydrogen bonds with DNA bases.[A257659] Intercalation of doxorubicin can introduce torsional stress into the polynucleotide structure, thus destabilizing nucleosome structures and leading to nucleosome eviction and replacement.[A257664,A18538] Additionally, the doxorubicin-DNA complex can interfere with topoisomerase II enzyme activity by preventing relegation of topoisomerase-mediated DNA breaks, thus inhibiting replication and transcription and inducing apoptosis.[A257669,A257674]   Moreover, doxorubicin can be metabolized by microsomal NADPH-cytochrome P-450 reductase into a semiquinone radical, which can be reoxidized in the presence of oxygen to form oxygen radicals.[A1579,A257584] Reactive oxygen species have been known to cause cellular damage through various mechanisms, including lipid peroxidation and membrane damage, DNA damage, oxidative stress, and apoptosis.[A257634] Although free radicals generated from this pathway can be deactivated by catalase and superoxide dismutase, tumor and myocardial cells tend to lack these enzymes, thus explaining doxorubicin's effectiveness against cancer cells and tendency to cause cardiotoxicity.[A1579,A257584,A1578]"
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
DM2 ADRIAMYCIN wwPDB ?
DM2 '(1S,3S)-3-glycoloyl-3,5,12-trihydroxy-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-α-L-lyxo-hexopyranoside' DrugBank ?
DM2 '(8S-cis)-10-((3-amino-2,3,6-trideoxy-α-L-lyxo-hexopyranosyl)oxy)-7,8,9,10-tetrahydro-6,8,11-trihydroxy-8-(hydroxyacetyl)-1-methoxy-5,12-naphthacenedione' DrugBank ?
DM2 14-hydroxydaunomycin DrugBank ?
DM2 14-hydroxydaunorubicine DrugBank ?
DM2 Doxorubicin DrugBank ?
DM2 'Doxorubicin nanoparticles' DrugBank ?
DM2 Doxorubicinum DrugBank ?
DM2 Hydroxydaunorubicin DrugBank ?
DM2 MTC-DOX DrugBank ?
DM2 'MTC-DOX for Injection' DrugBank ?
DM2 Adriablastina DrugBank 'International brand'
DM2 Adriblastin DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id DM2
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00997
_pdbe_chem_comp_drugbank_classification.parent Anthracyclines
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Anthracyclines
_pdbe_chem_comp_drugbank_classification.superclass 'Phenylpropanoids and polyketides'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as anthracyclines. These are polyketides containing a tetracenequinone ring structure with a sugar attached by glycosidic linkage.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
DM2 DB00997 'DNA topoisomerase 2-alpha' Humans P11388 yes 1
DM2 DB00997 'Telomerase reverse transcriptase' Humans O14746 yes 2
DM2 DB00997 'DNA topoisomerase 1' Humans P11387 yes 3
DM2 DB00997 'DNA topoisomerase 2-beta' Humans Q02880 yes 4
DM2 DB00997 'Nucleolar and coiled-body phosphoprotein 1' Humans Q14978 unknown 5
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
DM2 C1 C 17.000 3.287 1
DM2 C2 C 16.994 4.915 2
DM2 C3 C 15.575 5.712 3
DM2 C4 C 14.181 4.872 4
DM2 O4 O 12.865 5.591 5
DM2 C5 C 14.225 3.245 6
DM2 C6 C 12.887 2.438 7
DM2 O6 O 11.571 3.157 8
DM2 C7 C 12.930 0.876 9
DM2 C8 C 11.639 0.111 10
DM2 O8 O 10.332 0.846 11
DM2 C9 C 11.657 -1.389 12
DM2 C10 C 10.301 -2.165 13
DM2 O10 O 9.002 -1.415 14
DM2 C11 C 10.307 -3.728 15
DM2 C12 C 11.669 -4.493 16
DM2 O12 O 10.939 -5.804 17
DM2 C13 C 12.439 -5.780 18
DM2 O13 O 11.709 -7.091 19
DM2 C14 C 13.938 -5.757 20
DM2 O14 O 14.708 -7.045 21
DM2 C15 C 13.007 -3.686 22
DM2 C16 C 12.964 -2.124 23
DM2 C17 C 14.255 -1.359 24
DM2 O17 O 15.562 -2.094 25
DM2 C18 C 14.237 0.141 26
DM2 C19 C 15.593 0.917 27
DM2 O19 O 16.892 0.167 28
DM2 C20 C 15.587 2.479 29
DM2 C21 C 12.831 7.091 30
DM2 "C1'" C 7.702 -2.165 31
DM2 "C2'" C 6.404 -1.415 32
DM2 "C3'" C 5.104 -2.165 33
DM2 "N3'" N 3.805 -1.415 34
DM2 "C4'" C 5.104 -3.665 35
DM2 "O4'" O 3.805 -4.415 36
DM2 "C5'" C 6.404 -4.415 37
DM2 "O5'" O 7.702 -3.665 38
DM2 "C6'" C 6.404 -5.915 39
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
DM2 C1 C2 DOUBLE NONE 1
DM2 C1 C20 SINGLE NONE 2
DM2 C2 C3 SINGLE NONE 3
DM2 C3 C4 DOUBLE NONE 4
DM2 C4 O4 SINGLE NONE 5
DM2 C4 C5 SINGLE NONE 6
DM2 O4 C21 SINGLE NONE 7
DM2 C5 C6 SINGLE NONE 8
DM2 C5 C20 DOUBLE NONE 9
DM2 C6 O6 DOUBLE NONE 10
DM2 C6 C7 SINGLE NONE 11
DM2 C7 C8 DOUBLE NONE 12
DM2 C7 C18 SINGLE NONE 13
DM2 C8 O8 SINGLE NONE 14
DM2 C8 C9 SINGLE NONE 15
DM2 C9 C10 SINGLE NONE 16
DM2 C9 C16 DOUBLE NONE 17
DM2 C10 O10 SINGLE BEGINDASH 18
DM2 C10 C11 SINGLE NONE 19
DM2 "C1'" O10 SINGLE BEGINDASH 20
DM2 C11 C12 SINGLE NONE 21
DM2 C12 O12 SINGLE BEGINDASH 22
DM2 C12 C13 SINGLE NONE 23
DM2 C12 C15 SINGLE NONE 24
DM2 C13 O13 DOUBLE NONE 25
DM2 C13 C14 SINGLE NONE 26
DM2 C14 O14 SINGLE NONE 27
DM2 C15 C16 SINGLE NONE 28
DM2 C16 C17 SINGLE NONE 29
DM2 C17 O17 SINGLE NONE 30
DM2 C17 C18 DOUBLE NONE 31
DM2 C18 C19 SINGLE NONE 32
DM2 C19 O19 DOUBLE NONE 33
DM2 C19 C20 SINGLE NONE 34
DM2 "C1'" "C2'" SINGLE NONE 35
DM2 "C1'" "O5'" SINGLE NONE 36
DM2 "C2'" "C3'" SINGLE NONE 37
DM2 "C3'" "N3'" SINGLE BEGINWEDGE 38
DM2 "C3'" "C4'" SINGLE NONE 39
DM2 "C4'" "O4'" SINGLE BEGINWEDGE 40
DM2 "C4'" "C5'" SINGLE NONE 41
DM2 "C5'" "O5'" SINGLE NONE 42
DM2 "C5'" "C6'" SINGLE BEGINWEDGE 43
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
DM2 MurckoScaffold S1 scaffold 'O=C1c2ccccc2C(=O)c2cc3c(cc21)CCC[C@@H]3O[C@H]1CCCCO1' InChI=1S/C23H22O4/c24-22-15-7-1-2-8-16(15)23(25)19-13-17-14(12-18(19)22)6-5-9-20(17)27-21-10-3-4-11-26-21/h1-2,7-8,12-13,20-21H,3-6,9-11H2/t20-,21-/m0/s1 QLPWHRZKZGFYTJ-SFTDATJTSA-N
DM2 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
DM2 pyranose F2 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
DM2 C1 S1 1
DM2 C2 S1 1
DM2 C3 S1 1
DM2 C4 S1 1
DM2 C5 S1 1
DM2 C6 S1 1
DM2 O6 S1 1
DM2 C7 S1 1
DM2 C8 S1 1
DM2 C9 S1 1
DM2 C10 S1 1
DM2 O10 S1 1
DM2 C11 S1 1
DM2 C12 S1 1
DM2 C15 S1 1
DM2 C16 S1 1
DM2 C17 S1 1
DM2 C18 S1 1
DM2 C19 S1 1
DM2 O19 S1 1
DM2 C20 S1 1
DM2 "C1'" S1 1
DM2 "C2'" S1 1
DM2 "C3'" S1 1
DM2 "C4'" S1 1
DM2 "C5'" S1 1
DM2 "O5'" S1 1
DM2 C1 F1 1
DM2 C2 F1 1
DM2 C3 F1 1
DM2 C4 F1 1
DM2 C5 F1 1
DM2 C20 F1 1
DM2 C7 F1 2
DM2 C8 F1 2
DM2 C9 F1 2
DM2 C16 F1 2
DM2 C17 F1 2
DM2 C18 F1 2
DM2 "C4'" F2 1
DM2 "C5'" F2 1
DM2 "O5'" F2 1
DM2 "C1'" F2 1
DM2 "C2'" F2 1
DM2 "C3'" F2 1
DM2 O10 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DM2
_pdbe_chem_comp_rdkit_properties.exactmw 543.174
_pdbe_chem_comp_rdkit_properties.amw 543.525
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 12
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 7
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 13
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 12
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 39
_pdbe_chem_comp_rdkit_properties.NumAtoms 68
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 12
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.444
_pdbe_chem_comp_rdkit_properties.NumRings 5
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 6
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 263.375
_pdbe_chem_comp_rdkit_properties.tpsa 206.070
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.714
_pdbe_chem_comp_rdkit_properties.CrippenMR 128.328
_pdbe_chem_comp_rdkit_properties.chi0v 18.438
_pdbe_chem_comp_rdkit_properties.chi1v 10.081
_pdbe_chem_comp_rdkit_properties.chi2v 5.521
_pdbe_chem_comp_rdkit_properties.chi3v 5.521
_pdbe_chem_comp_rdkit_properties.chi4v 3.832
_pdbe_chem_comp_rdkit_properties.chi0n 47.438
_pdbe_chem_comp_rdkit_properties.chi1n 24.017
_pdbe_chem_comp_rdkit_properties.chi2n 5.521
_pdbe_chem_comp_rdkit_properties.chi3n 5.521
_pdbe_chem_comp_rdkit_properties.chi4n 3.832
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.390
_pdbe_chem_comp_rdkit_properties.kappa1 9.062
_pdbe_chem_comp_rdkit_properties.kappa2 9.662
_pdbe_chem_comp_rdkit_properties.kappa3 4.112
_pdbe_chem_comp_rdkit_properties.Phi 2.245
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
DM2 UniChem DrugBank DB00997
DM2 UniChem 'Guide to Pharmacology' 7069
DM2 UniChem 'KEGG LIGAND' C01661
DM2 UniChem ChEBI 28748
DM2 UniChem ZINC ZINC000003918087
DM2 UniChem eMolecules 36788175
DM2 UniChem atlas doxorubicin
DM2 UniChem fdasrs 80168379AG
DM2 UniChem SureChEMBL SCHEMBL3243
DM2 UniChem PharmGKB PA449412
DM2 UniChem HMDB HMDB0015132
DM2 UniChem 'PubChem TPHARMA' 14910387
DM2 UniChem NMRShiftDB 60023387
DM2 UniChem LINCS LSM-4062
DM2 UniChem Nikkaji J3.792C
DM2 UniChem BindingDb 22984
DM2 UniChem BindingDb 32022
DM2 UniChem 'EPA CompTox Dashboard' DTXSID8021480
DM2 UniChem DrugCentral 960
DM2 UniChem MetaboLights MTBLC28748
DM2 UniChem BRENDA 127575
DM2 UniChem BRENDA 2134
DM2 UniChem BRENDA 229404
DM2 UniChem BRENDA 229405
DM2 UniChem BRENDA 32211
DM2 UniChem BRENDA 49017
DM2 UniChem DailyMed DOXORUBICIN
DM2 UniChem ClinicalTrials ADRIAMYCIN
DM2 UniChem ClinicalTrials ADRIBLASTINA
DM2 UniChem ClinicalTrials CAELYX
DM2 UniChem ClinicalTrials DOXIL
DM2 UniChem ClinicalTrials DOXORUBICIN
DM2 UniChem ClinicalTrials 'DOXORUBICIN HYDROCHLORIDE'
DM2 UniChem ClinicalTrials 'LIPOSOMAL DOXORUBICIN HYDROCHLORIDE'
DM2 UniChem ClinicalTrials NSC-123127
DM2 UniChem ClinicalTrials RUBEX
DM2 UniChem rxnorm ADRIAMYCIN
DM2 UniChem rxnorm DOXIL
DM2 UniChem rxnorm DOXORUBICIN
DM2 UniChem rxnorm 'DOXORUBICIN HYDROCHLORIDE'
DM2 UniChem 'Probes And Drugs' PD003620
DM2 UniChem ACTor 23214-92-8
DM2 UniChem 'PubChem TPHARMA' 14910388
DM2 UniChem PubChem 31703
DM2 UniChem Mcule MCULE-4188577717
DM2 UniChem ACTor 111266-55-8
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
DM2 C1 6.323 -0.749 0.249 ETKDGv3 1
DM2 C2 6.929 -1.936 0.178 ETKDGv3 2
DM2 C3 6.208 -3.104 -0.350 ETKDGv3 3
DM2 C4 4.933 -2.991 -0.770 ETKDGv3 4
DM2 O4 4.214 -4.099 -1.254 ETKDGv3 5
DM2 C5 4.254 -1.658 -0.708 ETKDGv3 6
DM2 C6 2.870 -1.497 -1.219 ETKDGv3 7
DM2 O6 2.420 -2.327 -2.054 ETKDGv3 8
DM2 C7 2.071 -0.301 -0.844 ETKDGv3 9
DM2 C8 0.724 -0.245 -0.972 ETKDGv3 10
DM2 O8 -0.042 -1.380 -1.257 ETKDGv3 11
DM2 C9 0.001 1.042 -0.779 ETKDGv3 12
DM2 C10 -1.507 1.035 -0.973 ETKDGv3 13
DM2 O10 -2.085 0.346 0.123 ETKDGv3 14
DM2 C11 -2.089 2.459 -1.086 ETKDGv3 15
DM2 C12 -1.550 3.375 0.022 ETKDGv3 16
DM2 O12 -1.841 2.799 1.276 ETKDGv3 17
DM2 C13 -2.261 4.728 -0.068 ETKDGv3 18
DM2 O13 -3.465 4.769 0.143 ETKDGv3 19
DM2 C14 -1.563 6.015 -0.425 ETKDGv3 20
DM2 O14 -1.299 6.038 -1.799 ETKDGv3 21
DM2 C15 -0.015 3.475 -0.156 ETKDGv3 22
DM2 C16 0.680 2.140 -0.358 ETKDGv3 23
DM2 C17 2.165 2.067 -0.189 ETKDGv3 24
DM2 O17 2.896 3.209 0.157 ETKDGv3 25
DM2 C18 2.816 0.896 -0.378 ETKDGv3 26
DM2 C19 4.279 0.746 -0.128 ETKDGv3 27
DM2 O19 4.987 1.745 0.173 ETKDGv3 28
DM2 C20 4.920 -0.589 -0.209 ETKDGv3 29
DM2 C21 4.728 -5.423 -1.365 ETKDGv3 30
DM2 "C1'" -3.358 -0.210 -0.182 ETKDGv3 31
DM2 "C2'" -3.256 -1.735 -0.351 ETKDGv3 32
DM2 "C3'" -2.751 -2.428 0.933 ETKDGv3 33
DM2 "N3'" -3.389 -3.742 1.074 ETKDGv3 34
DM2 "C4'" -2.993 -1.542 2.181 ETKDGv3 35
DM2 "O4'" -3.080 -2.324 3.347 ETKDGv3 36
DM2 "C5'" -4.247 -0.633 2.020 ETKDGv3 37
DM2 "O5'" -4.284 0.158 0.831 ETKDGv3 38
DM2 "C6'" -5.560 -1.418 2.138 ETKDGv3 39
DM2 H1 6.871 0.096 0.648 ETKDGv3 40
DM2 H2 7.952 -2.043 0.514 ETKDGv3 41
DM2 H3 6.731 -4.050 -0.379 ETKDGv3 42
DM2 HO8 0.280 -2.328 -1.113 ETKDGv3 43
DM2 H10 -1.707 0.506 -1.935 ETKDGv3 44
DM2 H111 -3.199 2.418 -1.042 ETKDGv3 45
DM2 H112 -1.822 2.881 -2.081 ETKDGv3 46
DM2 HO12 -1.514 3.418 1.981 ETKDGv3 47
DM2 H141 -0.620 6.115 0.156 ETKDGv3 48
DM2 H142 -2.213 6.879 -0.160 ETKDGv3 49
DM2 HO14 -0.814 6.886 -1.972 ETKDGv3 50
DM2 H151 0.395 3.976 0.746 ETKDGv3 51
DM2 H152 0.230 4.095 -1.044 ETKDGv3 52
DM2 HO17 2.504 4.139 0.203 ETKDGv3 53
DM2 H211 5.600 -5.438 -2.053 ETKDGv3 54
DM2 H212 5.022 -5.804 -0.364 ETKDGv3 55
DM2 H213 3.939 -6.084 -1.778 ETKDGv3 56
DM2 "H1'" -3.781 0.178 -1.138 ETKDGv3 57
DM2 "H2'1" -4.265 -2.116 -0.624 ETKDGv3 58
DM2 "H2'2" -2.584 -1.976 -1.201 ETKDGv3 59
DM2 "H3'" -1.651 -2.579 0.834 ETKDGv3 60
DM2 "HN'1" -2.880 -4.281 1.812 ETKDGv3 61
DM2 "HN'2" -3.239 -4.279 0.189 ETKDGv3 62
DM2 "H4'" -2.108 -0.871 2.287 ETKDGv3 63
DM2 "HO4'" -2.986 -1.705 4.118 ETKDGv3 64
DM2 "H5'" -4.233 0.080 2.874 ETKDGv3 65
DM2 "H6'1" -5.619 -1.940 3.116 ETKDGv3 66
DM2 "H6'2" -6.420 -0.719 2.070 ETKDGv3 67
DM2 "H6'3" -5.654 -2.165 1.324 ETKDGv3 68
#