data_DM1 # _chem_comp.id DM1 _chem_comp.name DAUNOMYCIN _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAD _chem_comp.formula "C27 H29 N O10" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms DAUNORUBICIN _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2020-06-17 _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 527.520 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DM1 _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 1D11 _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 DM1 C1 C1 C 0 1 Y N N 15.076 18.210 5.093 -0.723 -0.349 6.044 C1 DM1 1 DM1 C2 C2 C 0 1 Y N N 16.284 18.936 5.143 0.243 0.085 6.939 C2 DM1 2 DM1 C3 C3 C 0 1 Y N N 17.527 18.293 5.081 1.488 0.476 6.492 C3 DM1 3 DM1 C4 C4 C 0 1 Y N N 17.520 16.910 5.002 1.792 0.441 5.134 C4 DM1 4 DM1 O4 O4 O 0 1 N N N 18.754 16.294 4.969 3.017 0.827 4.699 O4 DM1 5 DM1 C5 C5 C 0 1 Y N N 16.334 16.176 4.980 0.826 0.012 4.221 C5 DM1 6 DM1 C6 C6 C 0 1 N N N 16.306 14.768 4.911 1.126 -0.038 2.777 C6 DM1 7 DM1 O6 O6 O 0 1 N N N 17.462 14.041 4.823 2.273 0.058 2.382 O6 DM1 8 DM1 C7 C7 C 0 1 Y N N 15.089 14.049 4.912 0.018 -0.201 1.818 C7 DM1 9 DM1 C8 C8 C 0 1 Y N N 15.065 12.635 4.850 0.208 0.035 0.459 C8 DM1 10 DM1 O8 O8 O 0 1 N N N 16.272 11.915 4.864 1.428 0.419 0.007 O8 DM1 11 DM1 C9 C9 C 0 1 Y N N 13.847 11.929 4.810 -0.851 -0.118 -0.444 C9 DM1 12 DM1 C10 C10 C 0 1 N N S 13.931 10.456 4.819 -0.569 0.164 -1.897 C10 DM1 13 DM1 O10 O10 O 0 1 N N N 14.546 10.208 6.171 0.699 -0.393 -2.246 O10 DM1 14 DM1 C11 C11 C 0 1 N N N 12.603 9.711 4.699 -1.649 -0.447 -2.785 C11 DM1 15 DM1 C12 C12 C 0 1 N N S 11.442 10.539 5.370 -3.018 -0.005 -2.254 C12 DM1 16 DM1 O12 O12 O 0 1 N N N 11.531 10.603 6.805 -4.038 -0.375 -3.184 O12 DM1 17 DM1 C13 C13 C 0 1 N N N 10.153 9.725 5.149 -3.029 1.487 -2.055 C13 DM1 18 DM1 O13 O13 O 0 1 N N N 9.415 10.008 4.095 -2.773 1.954 -0.971 O13 DM1 19 DM1 C14 C14 C 0 1 N N N 9.798 8.587 6.083 -3.358 2.399 -3.209 C14 DM1 20 DM1 C15 C15 C 0 1 N N N 11.346 11.979 4.813 -3.262 -0.705 -0.918 C15 DM1 21 DM1 C16 C16 C 0 1 Y N N 12.679 12.633 4.852 -2.087 -0.511 0.004 C16 DM1 22 DM1 C17 C17 C 0 1 Y N N 12.674 14.045 4.878 -2.295 -0.754 1.369 C17 DM1 23 DM1 O17 O17 O 0 1 N N N 11.428 14.623 4.847 -3.519 -1.140 1.806 O17 DM1 24 DM1 C18 C18 C 0 1 Y N N 13.866 14.761 4.931 -1.252 -0.601 2.280 C18 DM1 25 DM1 C19 C19 C 0 1 N N N 13.865 16.186 4.984 -1.461 -0.851 3.718 C19 DM1 26 DM1 O19 O19 O 0 1 N N N 12.738 16.887 5.004 -2.460 -1.427 4.104 O19 DM1 27 DM1 C20 C20 C 0 1 Y N N 15.112 16.834 4.999 -0.440 -0.391 4.685 C20 DM1 28 DM1 C21 C21 C 0 1 N N N 19.976 17.161 5.150 3.763 1.211 5.855 C21 DM1 29 DM1 "C1'" C1* C 0 1 N N R 15.484 9.139 6.380 1.456 0.653 -2.858 "C1'" DM1 30 DM1 "C2'" C2* C 0 1 N N N 16.539 9.605 7.374 2.919 0.220 -2.976 "C2'" DM1 31 DM1 "C3'" C3* C 0 1 N N S 15.948 9.604 8.804 2.995 -1.062 -3.812 "C3'" DM1 32 DM1 "N3'" N3* N 0 1 N N N 16.975 9.929 9.802 4.402 -1.404 -4.061 "N3'" DM1 33 DM1 "C4'" C4* C 0 1 N N S 15.066 8.368 9.128 2.276 -0.822 -5.144 "C4'" DM1 34 DM1 "O4'" O4* O 0 1 N N N 16.035 7.236 9.128 2.994 0.148 -5.907 "O4'" DM1 35 DM1 "C5'" C5* C 0 1 N N S 14.045 8.040 7.988 0.861 -0.311 -4.862 "C5'" DM1 36 DM1 "O5'" O5* O 0 1 N N N 14.723 7.953 6.669 0.927 0.923 -4.155 "O5'" DM1 37 DM1 "C6'" C6* C 0 1 N N N 13.253 6.745 8.148 0.124 -0.100 -6.186 "C6'" DM1 38 DM1 H1 H1 H 0 1 N N N 14.098 18.720 5.127 -1.694 -0.654 6.405 H1 DM1 39 DM1 H2 H2 H 0 1 N N N 16.255 20.035 5.232 0.019 0.116 7.995 H2 DM1 40 DM1 H3 H3 H 0 1 N N N 18.476 18.854 5.093 2.231 0.811 7.200 H3 DM1 41 DM1 HO8 HO8 H 0 1 N N N 16.255 10.966 4.822 1.428 1.386 -0.008 HO8 DM1 42 DM1 H10 H10 H 0 1 N N N 14.494 10.079 3.933 -0.542 1.242 -2.054 H10 DM1 43 DM1 H111 1H11 H 0 0 N N N 12.368 9.450 3.640 -1.577 -1.534 -2.755 H111 DM1 44 DM1 H112 2H11 H 0 0 N N N 12.668 8.678 5.113 -1.523 -0.098 -3.810 H112 DM1 45 DM1 HO12 2HO1 H 0 0 N N N 10.831 11.102 7.209 -4.880 -0.095 -2.801 HO12 DM1 46 DM1 H141 1H14 H 0 0 N N N 8.865 7.997 5.923 -3.316 3.436 -2.876 H141 DM1 47 DM1 H142 2H14 H 0 0 N N N 10.658 7.878 6.115 -2.636 2.245 -4.011 H142 DM1 48 DM1 H143 3H14 H 0 0 N N N 9.790 8.979 7.126 -4.360 2.175 -3.574 H143 DM1 49 DM1 H151 1H15 H 0 0 N N N 10.900 12.001 3.791 -3.410 -1.770 -1.093 H151 DM1 50 DM1 H152 2H15 H 0 0 N N N 10.571 12.580 5.343 -4.156 -0.289 -0.454 H152 DM1 51 DM1 HO17 7HO1 H 0 0 N N N 11.424 15.572 4.864 -4.008 -0.333 2.017 HO17 DM1 52 DM1 H211 1H21 H 0 0 N N N 20.973 16.663 5.123 4.761 1.531 5.554 H211 DM1 53 DM1 H212 2H21 H 0 0 N N N 19.956 17.984 4.398 3.255 2.033 6.360 H212 DM1 54 DM1 H213 3H21 H 0 0 N N N 19.879 17.738 6.098 3.843 0.362 6.534 H213 DM1 55 DM1 "H1'" H1* H 0 1 N N N 16.096 8.856 5.492 1.392 1.552 -2.246 "H1'" DM1 56 DM1 "H2'1" 1H2* H 0 0 N N N 17.474 9.001 7.306 3.494 1.008 -3.463 "H2'1" DM1 57 DM1 "H2'2" 2H2* H 0 0 N N N 16.966 10.597 7.097 3.325 0.033 -1.982 "H2'2" DM1 58 DM1 "H3'" H3* H 0 1 N N N 15.205 10.434 8.855 2.510 -1.877 -3.275 "H3'" DM1 59 DM1 "HN'1" 1HN* H 0 0 N N N 16.585 9.928 10.744 4.832 -1.539 -3.159 "HN'1" DM1 60 DM1 "HN'2" 2HN* H 0 0 N N N 17.439 10.811 9.588 4.404 -2.303 -4.521 "HN'2" DM1 61 DM1 "H4'" H4* H 0 1 N N N 14.496 8.542 10.070 2.222 -1.757 -5.702 "H4'" DM1 62 DM1 "HO4'" *HO4 H 0 0 N N N 15.495 6.479 9.326 2.509 0.268 -6.735 "HO4'" DM1 63 DM1 "H5'" H5* H 0 1 N N N 13.326 8.889 8.054 0.324 -1.045 -4.261 "H5'" DM1 64 DM1 "H6'1" 1H6* H 0 0 N N N 12.525 6.511 7.335 -0.883 0.263 -5.986 "H6'1" DM1 65 DM1 "H6'2" 2H6* H 0 0 N N N 13.953 5.888 8.285 0.662 0.631 -6.789 "H6'2" DM1 66 DM1 "H6'3" 3H6* H 0 0 N N N 12.732 6.739 9.134 0.068 -1.045 -6.726 "H6'3" DM1 67 # # 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 DM1 C1 C2 DOUB Y N 1 DM1 C1 C20 SING Y N 2 DM1 C1 H1 SING N N 3 DM1 C2 C3 SING Y N 4 DM1 C2 H2 SING N N 5 DM1 C3 C4 DOUB Y N 6 DM1 C3 H3 SING N N 7 DM1 C4 O4 SING N N 8 DM1 C4 C5 SING Y N 9 DM1 O4 C21 SING N N 10 DM1 C5 C6 SING N N 11 DM1 C5 C20 DOUB Y N 12 DM1 C6 O6 DOUB N N 13 DM1 C6 C7 SING N N 14 DM1 C7 C8 DOUB Y N 15 DM1 C7 C18 SING Y N 16 DM1 C8 O8 SING N N 17 DM1 C8 C9 SING Y N 18 DM1 O8 HO8 SING N N 19 DM1 C9 C10 SING N N 20 DM1 C9 C16 DOUB Y N 21 DM1 C10 O10 SING N N 22 DM1 C10 C11 SING N N 23 DM1 C10 H10 SING N N 24 DM1 O10 "C1'" SING N N 25 DM1 C11 C12 SING N N 26 DM1 C11 H111 SING N N 27 DM1 C11 H112 SING N N 28 DM1 C12 O12 SING N N 29 DM1 C12 C13 SING N N 30 DM1 C12 C15 SING N N 31 DM1 O12 HO12 SING N N 32 DM1 C13 O13 DOUB N N 33 DM1 C13 C14 SING N N 34 DM1 C14 H141 SING N N 35 DM1 C14 H142 SING N N 36 DM1 C14 H143 SING N N 37 DM1 C15 C16 SING N N 38 DM1 C15 H151 SING N N 39 DM1 C15 H152 SING N N 40 DM1 C16 C17 SING Y N 41 DM1 C17 O17 SING N N 42 DM1 C17 C18 DOUB Y N 43 DM1 O17 HO17 SING N N 44 DM1 C18 C19 SING N N 45 DM1 C19 O19 DOUB N N 46 DM1 C19 C20 SING N N 47 DM1 C21 H211 SING N N 48 DM1 C21 H212 SING N N 49 DM1 C21 H213 SING N N 50 DM1 "C1'" "C2'" SING N N 51 DM1 "C1'" "O5'" SING N N 52 DM1 "C1'" "H1'" SING N N 53 DM1 "C2'" "C3'" SING N N 54 DM1 "C2'" "H2'1" SING N N 55 DM1 "C2'" "H2'2" SING N N 56 DM1 "C3'" "N3'" SING N N 57 DM1 "C3'" "C4'" SING N N 58 DM1 "C3'" "H3'" SING N N 59 DM1 "N3'" "HN'1" SING N N 60 DM1 "N3'" "HN'2" SING N N 61 DM1 "C4'" "O4'" SING N N 62 DM1 "C4'" "C5'" SING N N 63 DM1 "C4'" "H4'" SING N N 64 DM1 "O4'" "HO4'" SING N N 65 DM1 "C5'" "O5'" SING N N 66 DM1 "C5'" "C6'" SING N N 67 DM1 "C5'" "H5'" SING N N 68 DM1 "C6'" "H6'1" SING N N 69 DM1 "C6'" "H6'2" SING N N 70 DM1 "C6'" "H6'3" SING N N 71 # # 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 DM1 SMILES ACDLabs 10.04 "O=C2c1c(O)c5c(c(O)c1C(=O)c3cccc(OC)c23)CC(O)(C(=O)C)CC5OC4OC(C(O)C(N)C4)C" DM1 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(C)=O" DM1 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(C)=O" DM1 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)C)O)N)O" DM1 SMILES "OpenEye OEToolkits" 1.5.0 "CC1C(C(CC(O1)OC2CC(Cc3c2c(c4c(c3O)C(=O)c5cccc(c5C4=O)OC)O)(C(=O)C)O)N)O" DM1 InChI InChI 1.03 "InChI=1S/C27H29NO10/c1-10-22(30)14(28)7-17(37-10)38-16-9-27(35,11(2)29)8-13-19(16)26(34)21-20(24(13)32)23(31)12-5-4-6-15(36-3)18(12)25(21)33/h4-6,10,14,16-17,22,30,32,34-35H,7-9,28H2,1-3H3/t10-,14-,16-,17-,22+,27-/m0/s1" DM1 InChIKey InChI 1.03 STQGQHZAVUOBTE-VGBVRHCVSA-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 DM1 "SYSTEMATIC NAME" ACDLabs 10.04 "(1S,3S)-3-acetyl-3,5,12-trihydroxy-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside" DM1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(7S,9S)-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl-oxan-2-yl]oxy-9-ethanoyl-6,9,11-trihydroxy-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 DM1 "Create component" 1999-07-08 RCSB DM1 "Modify descriptor" 2011-06-04 RCSB DM1 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id DM1 _pdbx_chem_comp_synonyms.name DAUNORUBICIN _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##