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.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
DM1 C1 C1 C 0 1 Y N N N 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 N 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 N 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 N 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 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 N 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 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 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 N 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 N 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 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 N 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 N N N 13.931 10.456 4.819 -0.569 0.164 -1.897 C10 DM1 13
DM1 O10 O10 O 0 1 N N N 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 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 N N N 11.442 10.539 5.370 -3.018 -0.005 -2.254 C12 DM1 16
DM1 O12 O12 O 0 1 N N N 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 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 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 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 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 N 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 N 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 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 N 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 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 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 N 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 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 N N N 15.484 9.139 6.380 1.456 0.653 -2.858 "C1'" DM1 30
DM1 "C2'" C2* C 0 1 N N N 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 N N N 15.948 9.604 8.804 2.995 -1.062 -3.812 "C3'" DM1 32
DM1 "N3'" N3* N 0 1 N N N 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 N N N 15.066 8.368 9.128 2.276 -0.822 -5.144 "C4'" DM1 34
DM1 "O4'" O4* O 0 1 N N N 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 N N N 14.045 8.040 7.988 0.861 -0.311 -4.862 "C5'" DM1 36
DM1 "O5'" O5* O 0 1 N N N 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ?
#
_pdbe_chem_comp_drugbank_details.comp_id DM1
_pdbe_chem_comp_drugbank_details.drugbank_id DB00694
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Daunorubicin
_pdbe_chem_comp_drugbank_details.description
'A very toxic anthracycline aminoglycoside antineoplastic isolated from Streptomyces peucetius and others, used in treatment of leukemia and other neoplasms.'
_pdbe_chem_comp_drugbank_details.cas_number 20830-81-3
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Daunorubicin has antimitotic and cytotoxic activity through a number of proposed mechanisms of action: Daunorubicin forms complexes with DNA by intercalation between base pairs, and it inhibits topoisomerase II activity by stabilizing the DNA-topoisomerase II complex, preventing the religation portion of the ligation-religation reaction that topoisomerase II catalyzes.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
DM1 DAUNORUBICIN wwPDB ?
DM1 (+)-Daunomycin DrugBank ?
DM1 '(8S-cis)-8-acetyl-10-((3-amino-2,3,6-trideoxy-α-L-lyxo-hexopyrannosyl)oxy)-7,8,9,10-tetrahydro-6,8,11-trihydroxy-1-methoxy-5,12-napthacenedione' DrugBank ?
DM1 Acetyladriamycin DrugBank ?
DM1 Daunomycin DrugBank ?
DM1 Daunorubicin DrugBank ?
DM1 'Daunorubicin liposomal' DrugBank ?
DM1 Daunorubicinum DrugBank ?
DM1 'Leukaemomycin C' DrugBank ?
DM1 Rubidomycin DrugBank ?
DM1 Cerubidin DrugBank 'International brand'
DM1 'Cérubidine' DrugBank 'International brand'
DM1 Daunoblastin DrugBank 'International brand'
DM1 Daunoblastina DrugBank 'International brand'
DM1 Daunorrubicina DrugBank 'International brand'
DM1 Maxidauno DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id DM1
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00694
_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
DM1 DB00694 'DNA topoisomerase 2-alpha' Humans P11388 yes 1
DM1 DB00694 'DNA topoisomerase 2-beta' Humans Q02880 yes 2
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
DM1 C1 C 17.000 3.287 1
DM1 C2 C 16.994 4.915 2
DM1 C3 C 15.575 5.712 3
DM1 C4 C 14.181 4.872 4
DM1 O4 O 12.865 5.591 5
DM1 C5 C 14.225 3.245 6
DM1 C6 C 12.887 2.438 7
DM1 O6 O 11.571 3.157 8
DM1 C7 C 12.930 0.876 9
DM1 C8 C 11.639 0.111 10
DM1 O8 O 10.332 0.846 11
DM1 C9 C 11.657 -1.389 12
DM1 C10 C 10.301 -2.165 13
DM1 O10 O 9.002 -1.415 14
DM1 C11 C 10.307 -3.728 15
DM1 C12 C 11.669 -4.493 16
DM1 O12 O 10.939 -5.804 17
DM1 C13 C 12.439 -5.780 18
DM1 O13 O 11.709 -7.091 19
DM1 C14 C 13.938 -5.757 20
DM1 C15 C 13.007 -3.686 21
DM1 C16 C 12.964 -2.124 22
DM1 C17 C 14.255 -1.359 23
DM1 O17 O 15.562 -2.094 24
DM1 C18 C 14.237 0.141 25
DM1 C19 C 15.593 0.917 26
DM1 O19 O 16.892 0.167 27
DM1 C20 C 15.587 2.479 28
DM1 C21 C 12.831 7.091 29
DM1 "C1'" C 7.702 -2.165 30
DM1 "C2'" C 6.404 -1.415 31
DM1 "C3'" C 5.104 -2.165 32
DM1 "N3'" N 3.805 -1.415 33
DM1 "C4'" C 5.104 -3.665 34
DM1 "O4'" O 3.805 -4.415 35
DM1 "C5'" C 6.404 -4.415 36
DM1 "O5'" O 7.702 -3.665 37
DM1 "C6'" C 6.404 -5.915 38
#
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
DM1 C1 C2 DOUBLE NONE 1
DM1 C1 C20 SINGLE NONE 2
DM1 C2 C3 SINGLE NONE 3
DM1 C3 C4 DOUBLE NONE 4
DM1 C4 O4 SINGLE NONE 5
DM1 C4 C5 SINGLE NONE 6
DM1 O4 C21 SINGLE NONE 7
DM1 C5 C6 SINGLE NONE 8
DM1 C5 C20 DOUBLE NONE 9
DM1 C6 O6 DOUBLE NONE 10
DM1 C6 C7 SINGLE NONE 11
DM1 C7 C8 DOUBLE NONE 12
DM1 C7 C18 SINGLE NONE 13
DM1 C8 O8 SINGLE NONE 14
DM1 C8 C9 SINGLE NONE 15
DM1 C9 C10 SINGLE NONE 16
DM1 C9 C16 DOUBLE NONE 17
DM1 C10 O10 SINGLE BEGINDASH 18
DM1 C10 C11 SINGLE NONE 19
DM1 "C1'" O10 SINGLE BEGINDASH 20
DM1 C11 C12 SINGLE NONE 21
DM1 C12 O12 SINGLE BEGINDASH 22
DM1 C12 C13 SINGLE NONE 23
DM1 C12 C15 SINGLE NONE 24
DM1 C13 O13 DOUBLE NONE 25
DM1 C13 C14 SINGLE NONE 26
DM1 C15 C16 SINGLE NONE 27
DM1 C16 C17 SINGLE NONE 28
DM1 C17 O17 SINGLE NONE 29
DM1 C17 C18 DOUBLE NONE 30
DM1 C18 C19 SINGLE NONE 31
DM1 C19 O19 DOUBLE NONE 32
DM1 C19 C20 SINGLE NONE 33
DM1 "C1'" "C2'" SINGLE NONE 34
DM1 "C1'" "O5'" SINGLE NONE 35
DM1 "C2'" "C3'" SINGLE NONE 36
DM1 "C3'" "N3'" SINGLE BEGINWEDGE 37
DM1 "C3'" "C4'" SINGLE NONE 38
DM1 "C4'" "O4'" SINGLE BEGINWEDGE 39
DM1 "C4'" "C5'" SINGLE NONE 40
DM1 "C5'" "O5'" SINGLE NONE 41
DM1 "C5'" "C6'" SINGLE BEGINWEDGE 42
#
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
DM1 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
DM1 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
DM1 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
DM1 C1 S1 1
DM1 C2 S1 1
DM1 C3 S1 1
DM1 C4 S1 1
DM1 C5 S1 1
DM1 C6 S1 1
DM1 O6 S1 1
DM1 C7 S1 1
DM1 C8 S1 1
DM1 C9 S1 1
DM1 C10 S1 1
DM1 O10 S1 1
DM1 C11 S1 1
DM1 C12 S1 1
DM1 C15 S1 1
DM1 C16 S1 1
DM1 C17 S1 1
DM1 C18 S1 1
DM1 C19 S1 1
DM1 O19 S1 1
DM1 C20 S1 1
DM1 "C1'" S1 1
DM1 "C2'" S1 1
DM1 "C3'" S1 1
DM1 "C4'" S1 1
DM1 "C5'" S1 1
DM1 "O5'" S1 1
DM1 C1 F1 1
DM1 C2 F1 1
DM1 C3 F1 1
DM1 C4 F1 1
DM1 C5 F1 1
DM1 C20 F1 1
DM1 C7 F1 2
DM1 C8 F1 2
DM1 C9 F1 2
DM1 C16 F1 2
DM1 C17 F1 2
DM1 C18 F1 2
DM1 "C4'" F2 1
DM1 "C5'" F2 1
DM1 "O5'" F2 1
DM1 "C1'" F2 1
DM1 "C2'" F2 1
DM1 "C3'" F2 1
DM1 O10 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DM1
_pdbe_chem_comp_rdkit_properties.exactmw 527.179
_pdbe_chem_comp_rdkit_properties.amw 527.526
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 11
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 11
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 38
_pdbe_chem_comp_rdkit_properties.NumAtoms 67
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11
_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 258.494
_pdbe_chem_comp_rdkit_properties.tpsa 185.840
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.687
_pdbe_chem_comp_rdkit_properties.CrippenMR 126.917
_pdbe_chem_comp_rdkit_properties.chi0v 18.030
_pdbe_chem_comp_rdkit_properties.chi1v 9.877
_pdbe_chem_comp_rdkit_properties.chi2v 5.428
_pdbe_chem_comp_rdkit_properties.chi3v 5.428
_pdbe_chem_comp_rdkit_properties.chi4v 3.760
_pdbe_chem_comp_rdkit_properties.chi0n 47.030
_pdbe_chem_comp_rdkit_properties.chi1n 23.905
_pdbe_chem_comp_rdkit_properties.chi2n 5.428
_pdbe_chem_comp_rdkit_properties.chi3n 5.428
_pdbe_chem_comp_rdkit_properties.chi4n 3.760
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.350
_pdbe_chem_comp_rdkit_properties.kappa1 8.573
_pdbe_chem_comp_rdkit_properties.kappa2 9.139
_pdbe_chem_comp_rdkit_properties.kappa3 3.810
_pdbe_chem_comp_rdkit_properties.Phi 2.062
#
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
DM1 UniChem ChEMBL CHEMBL178
DM1 UniChem DrugBank DB00694
DM1 UniChem PDBe DM1
DM1 UniChem 'Guide to Pharmacology' 7063
DM1 UniChem 'PubChem DOTF' 125299287
DM1 UniChem 'KEGG LIGAND' C01907
DM1 UniChem ChEBI 41977
DM1 UniChem ZINC ZINC000003917708
DM1 UniChem eMolecules 30152546
DM1 UniChem fdasrs ZS7284E0ZP
DM1 UniChem SureChEMBL SCHEMBL3041
DM1 UniChem PharmGKB PA449212
DM1 UniChem HMDB HMDB0014832
DM1 UniChem 'PubChem TPHARMA' 14763056
DM1 UniChem 'PubChem TPHARMA' 15481415
DM1 UniChem NMRShiftDB 60022097
DM1 UniChem LINCS LSM-2962
DM1 UniChem Nikkaji J3.149F
DM1 UniChem BindingDb 32017
DM1 UniChem BindingDb 50368352
DM1 UniChem 'EPA CompTox Dashboard' DTXSID7022883
DM1 UniChem LipidMaps LMPK13050002
DM1 UniChem DrugCentral 786
DM1 UniChem MetaboLights MTBLC41977
DM1 UniChem BRENDA 10631
DM1 UniChem BRENDA 1532
DM1 UniChem BRENDA 21578
DM1 UniChem BRENDA 229357
DM1 UniChem BRENDA 229358
DM1 UniChem BRENDA 229359
DM1 UniChem BRENDA 229360
DM1 UniChem BRENDA 249524
DM1 UniChem BRENDA 256870
DM1 UniChem BRENDA 48969
DM1 UniChem BRENDA 48970
DM1 UniChem BRENDA 48971
DM1 UniChem BRENDA 96463
DM1 UniChem ChemicalBook CB0338996
DM1 UniChem DailyMed DAUNORUBICIN
DM1 UniChem ClinicalTrials CERUBIDINE
DM1 UniChem ClinicalTrials DAUNORUBICIN
DM1 UniChem ClinicalTrials 'DAUNORUBICIN CITRATE'
DM1 UniChem ClinicalTrials 'DAUNORUBICIN HYDROCHLORIDE'
DM1 UniChem ClinicalTrials 'DAUNORUBICIN LIPOSOMAL'
DM1 UniChem ClinicalTrials DAUNOXOME
DM1 UniChem ClinicalTrials 'FI 6339'
DM1 UniChem ClinicalTrials FI-6339
DM1 UniChem ClinicalTrials NSC-82151
DM1 UniChem ClinicalTrials 'RP 13057'
DM1 UniChem ClinicalTrials RP-13057
DM1 UniChem rxnorm DAUNORUBICIN
DM1 UniChem rxnorm 'DAUNORUBICIN CITRATE'
DM1 UniChem rxnorm 'DAUNORUBICIN HYDROCHLORIDE'
DM1 UniChem MedChemExpress HY-13062A
DM1 UniChem 'Probes And Drugs' PD009842
DM1 UniChem ACTor 20830-81-3
DM1 UniChem PubChem 30323
DM1 UniChem ACTor 11006-54-5
DM1 UniChem ACTor 1407-15-4
#
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
DM1 C1 6.714 -0.375 -0.085 ETKDGv3 1
DM1 C2 7.340 -1.553 -0.037 ETKDGv3 2
DM1 C3 6.598 -2.798 -0.299 ETKDGv3 3
DM1 C4 5.283 -2.763 -0.593 ETKDGv3 4
DM1 O4 4.545 -3.938 -0.824 ETKDGv3 5
DM1 C5 4.582 -1.444 -0.662 ETKDGv3 6
DM1 C6 3.152 -1.369 -1.054 ETKDGv3 7
DM1 O6 2.652 -2.296 -1.747 ETKDGv3 8
DM1 C7 2.358 -0.152 -0.730 ETKDGv3 9
DM1 C8 1.003 -0.136 -0.712 ETKDGv3 10
DM1 O8 0.242 -1.305 -0.821 ETKDGv3 11
DM1 C9 0.271 1.148 -0.544 ETKDGv3 12
DM1 C10 -1.249 1.116 -0.612 ETKDGv3 13
DM1 O10 -1.735 0.519 0.583 ETKDGv3 14
DM1 C11 -1.864 2.520 -0.774 ETKDGv3 15
DM1 C12 -1.227 3.531 0.192 ETKDGv3 16
DM1 O12 -1.409 3.072 1.515 ETKDGv3 17
DM1 C13 -1.897 4.888 0.005 ETKDGv3 18
DM1 O13 -1.814 5.460 -1.073 ETKDGv3 19
DM1 C14 -2.666 5.549 1.114 ETKDGv3 20
DM1 C15 0.279 3.627 -0.140 ETKDGv3 21
DM1 C16 0.960 2.276 -0.241 ETKDGv3 22
DM1 C17 2.443 2.234 -0.134 ETKDGv3 23
DM1 O17 3.091 3.393 0.307 ETKDGv3 24
DM1 C18 3.116 1.094 -0.431 ETKDGv3 25
DM1 C19 4.601 1.013 -0.485 ETKDGv3 26
DM1 O19 5.302 2.043 -0.672 ETKDGv3 27
DM1 C20 5.268 -0.306 -0.406 ETKDGv3 28
DM1 C21 5.078 -5.259 -0.787 ETKDGv3 29
DM1 "C1'" -2.718 -0.467 0.323 ETKDGv3 30
DM1 "C2'" -3.036 -1.200 1.642 ETKDGv3 31
DM1 "C3'" -4.463 -1.791 1.641 ETKDGv3 32
DM1 "N3'" -4.522 -2.984 2.487 ETKDGv3 33
DM1 "C4'" -4.910 -2.117 0.203 ETKDGv3 34
DM1 "O4'" -4.089 -3.123 -0.342 ETKDGv3 35
DM1 "C5'" -4.836 -0.815 -0.655 ETKDGv3 36
DM1 "O5'" -3.891 0.143 -0.188 ETKDGv3 37
DM1 "C6'" -4.636 -1.081 -2.152 ETKDGv3 38
DM1 H1 7.273 0.530 0.117 ETKDGv3 39
DM1 H2 8.395 -1.597 0.199 ETKDGv3 40
DM1 H3 7.139 -3.732 -0.239 ETKDGv3 41
DM1 HO8 0.601 -2.233 -0.640 ETKDGv3 42
DM1 H10 -1.521 0.543 -1.532 ETKDGv3 43
DM1 H111 -1.712 2.856 -1.825 ETKDGv3 44
DM1 H112 -2.961 2.475 -0.601 ETKDGv3 45
DM1 HO12 -0.884 3.656 2.123 ETKDGv3 46
DM1 H141 -3.168 6.470 0.748 ETKDGv3 47
DM1 H142 -3.443 4.855 1.499 ETKDGv3 48
DM1 H143 -1.976 5.827 1.937 ETKDGv3 49
DM1 H151 0.420 4.138 -1.118 ETKDGv3 50
DM1 H152 0.777 4.254 0.630 ETKDGv3 51
DM1 HO17 4.021 3.406 0.703 ETKDGv3 52
DM1 H211 5.484 -5.479 0.223 ETKDGv3 53
DM1 H212 4.267 -5.982 -1.009 ETKDGv3 54
DM1 H213 5.874 -5.371 -1.554 ETKDGv3 55
DM1 "H1'" -2.314 -1.219 -0.395 ETKDGv3 56
DM1 "H2'1" -2.282 -2.005 1.788 ETKDGv3 57
DM1 "H2'2" -2.945 -0.497 2.500 ETKDGv3 58
DM1 "H3'" -5.161 -1.025 2.052 ETKDGv3 59
DM1 "HN'1" -4.270 -2.705 3.463 ETKDGv3 60
DM1 "HN'2" -5.516 -3.310 2.527 ETKDGv3 61
DM1 "H4'" -5.970 -2.465 0.215 ETKDGv3 62
DM1 "HO4'" -4.443 -3.993 -0.020 ETKDGv3 63
DM1 "H5'" -5.832 -0.328 -0.563 ETKDGv3 64
DM1 "H6'1" -4.711 -0.126 -2.715 ETKDGv3 65
DM1 "H6'2" -5.420 -1.773 -2.526 ETKDGv3 66
DM1 "H6'3" -3.637 -1.524 -2.350 ETKDGv3 67
#