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.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 15.226 18.450 4.896 -0.791 -0.376 6.114 C1 DM2 1 DM2 C2 C2 C 0 1 Y 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 17.654 18.469 4.880 1.331 0.630 6.611 C3 DM2 3 DM2 C4 C4 C 0 1 Y 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 18.898 16.388 4.808 2.887 1.062 4.859 O4 DM2 5 DM2 C5 C5 C 0 1 Y 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 16.409 14.946 4.803 1.136 0.008 2.900 C6 DM2 7 DM2 O6 O6 O 0 1 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 15.196 14.209 4.817 0.076 -0.262 1.910 C7 DM2 9 DM2 C8 C8 C 0 1 Y 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 16.295 12.032 4.788 1.493 0.428 0.131 O8 DM2 11 DM2 C9 C9 C 0 1 Y 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 13.995 10.639 4.786 -0.413 -0.024 -1.829 C10 DM2 13 DM2 O10 O10 O 0 1 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 12.711 9.868 4.523 -1.412 -0.739 -2.736 C11 DM2 15 DM2 C12 C12 C 0 1 N N S 11.569 10.600 5.359 -2.828 -0.395 -2.259 C12 DM2 16 DM2 O12 O12 O 0 1 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 10.269 9.864 5.071 -2.962 1.096 -2.096 C13 DM2 18 DM2 O13 O13 O 0 1 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 9.825 8.804 6.033 -3.323 1.954 -3.282 C14 DM2 20 DM2 O14 O14 O 0 1 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 11.432 12.065 4.766 -3.061 -1.082 -0.915 C15 DM2 22 DM2 C16 C16 C 0 1 Y 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 12.761 14.224 4.827 -2.170 -1.005 1.402 C17 DM2 24 DM2 O17 O17 O 0 1 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 13.985 14.924 4.822 -1.174 -0.751 2.341 C18 DM2 26 DM2 C19 C19 C 0 1 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 12.853 16.988 4.878 -2.373 -1.630 4.146 O19 DM2 28 DM2 C20 C20 C 0 1 Y 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 20.164 17.131 4.894 3.562 1.529 6.029 C21 DM2 30 DM2 "C1'" C1* C 0 1 N N R 15.508 9.325 6.325 1.598 0.601 -2.737 "C1'" DM2 31 DM2 "C2'" C2* C 0 1 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 15.986 9.896 8.700 3.298 -1.006 -3.599 "C3'" DM2 33 DM2 "N3'" N3* N 0 1 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 15.236 8.613 9.132 2.607 -0.854 -4.959 "C4'" DM2 35 DM2 "O4'" O4* O 0 1 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 14.150 8.254 8.082 1.148 -0.450 -4.735 "C5'" DM2 37 DM2 "O5'" O5* O 0 1 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 13.470 6.895 8.316 0.441 -0.326 -6.086 "C6'" DM2 39 DM2 H1 H1 H 0 1 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 16.411 20.263 4.942 -0.154 0.188 8.075 H2 DM2 41 DM2 H3 H3 H 0 1 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 16.273 11.082 4.765 1.418 1.392 0.091 HO8 DM2 43 DM2 H10 H10 H 0 1 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 12.469 9.766 3.439 -1.256 -1.816 -2.677 H111 DM2 45 DM2 H112 2H11 H 0 0 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 10.930 11.189 7.333 -4.658 -0.643 -2.862 HO12 DM2 47 DM2 H141 1H14 H 0 0 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 9.765 9.211 7.069 -4.291 1.643 -3.674 H142 DM2 49 DM2 HO14 4HO1 H 0 0 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 11.003 12.046 3.737 -3.120 -2.160 -1.068 H151 DM2 51 DM2 H152 2H15 H 0 0 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 11.591 15.838 4.815 -3.932 -0.707 1.985 HO17 DM2 53 DM2 H211 1H21 H 0 0 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 20.174 17.897 4.084 2.975 2.319 6.497 H212 DM2 55 DM2 H213 3H21 H 0 0 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 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 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 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 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 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 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 14.688 8.702 10.098 2.645 -1.802 -5.496 "H4'" DM2 63 DM2 "HO4'" *HO4 H 0 0 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 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 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 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 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 ? ##