data_QDM # _chem_comp.id QDM _chem_comp.name TDP-3,6-dideoxy-3-N,N-dimethylglucose _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H31 N3 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-02-17 _chem_comp.pdbx_modified_date 2014-02-21 _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 575.398 _chem_comp.one_letter_code ? _chem_comp.three_letter_code QDM _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4OQD _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 QDM O2A O2A O 0 1 N N N 11.761 8.365 17.033 0.384 -3.742 0.073 O2A QDM 1 QDM PA PA P 0 1 N N N 10.890 9.493 17.455 0.041 -2.436 -0.531 PA QDM 2 QDM O1A O1A O 0 1 N N N 9.474 9.158 17.993 -0.466 -2.661 -2.043 O1A QDM 3 QDM O3A O3A O 0 1 N N N 10.523 10.564 16.308 1.343 -1.488 -0.537 O3A QDM 4 QDM PB PB P 0 1 N N N 9.482 10.675 15.128 2.889 -1.714 -0.926 PB QDM 5 QDM O1B O1B O 0 1 N N N 8.685 11.936 15.300 3.056 -1.643 -2.525 O1B QDM 6 QDM O3B O3B O 0 1 N N N 10.553 10.869 13.826 3.787 -0.568 -0.240 O3B QDM 7 QDM C1Q C1Q C 0 1 N N R 11.274 12.064 13.804 5.215 -0.552 -0.310 C1Q QDM 8 QDM C2Q C2Q C 0 1 N N R 10.672 13.106 12.857 5.780 0.117 0.946 C2Q QDM 9 QDM O2Q O2Q O 0 1 N N N 9.364 13.535 13.343 5.321 -0.580 2.106 O2Q QDM 10 QDM C3Q C3Q C 0 1 N N S 10.499 12.587 11.418 5.301 1.571 1.000 C3Q QDM 11 QDM N3Q N3Q N 0 1 N N N 9.885 13.603 10.534 5.897 2.242 2.162 N3Q QDM 12 QDM C2M C2M C 0 1 N N N 9.325 13.007 9.310 7.329 2.493 1.948 C2M QDM 13 QDM C1M C1M C 0 1 N N N 10.900 14.648 10.221 5.185 3.489 2.473 C1M QDM 14 QDM C4Q C4Q C 0 1 N N S 11.808 11.937 10.920 5.732 2.287 -0.284 C4Q QDM 15 QDM O4Q O4Q O 0 1 N N N 11.602 11.297 9.667 5.228 3.624 -0.278 O4Q QDM 16 QDM C5Q C5Q C 0 1 N N R 12.323 11.006 12.047 5.169 1.534 -1.492 C5Q QDM 17 QDM C6Q C6Q C 0 1 N N N 13.776 10.568 11.702 5.645 2.208 -2.781 C6Q QDM 18 QDM O5Q O5Q O 0 1 N N N 12.576 11.636 13.258 5.628 0.180 -1.465 O5Q QDM 19 QDM O2B O2B O 0 1 N N N 8.857 9.359 14.886 3.330 -3.042 -0.442 O2B QDM 20 QDM "O5'" "O5'" O 0 1 N N N 11.599 10.402 18.525 -1.128 -1.737 0.328 "O5'" QDM 21 QDM "C5'" "C5'" C 0 1 N N N 11.046 11.555 19.150 -2.375 -2.375 0.609 "C5'" QDM 22 QDM "C4'" "C4'" C 0 1 N N R 11.867 12.777 18.818 -3.251 -1.438 1.443 "C4'" QDM 23 QDM "C3'" "C3'" C 0 1 N N S 13.255 12.703 19.431 -4.554 -2.153 1.864 "C3'" QDM 24 QDM "O3'" "O3'" O 0 1 N N N 14.210 13.366 18.572 -4.443 -2.649 3.200 "O3'" QDM 25 QDM "C2'" "C2'" C 0 1 N N N 13.162 13.382 20.777 -5.631 -1.048 1.785 "C2'" QDM 26 QDM "C1'" "C1'" C 0 1 N N R 12.122 14.427 20.462 -4.851 0.204 1.325 "C1'" QDM 27 QDM "O4'" "O4'" O 0 1 N N N 11.251 13.882 19.493 -3.687 -0.315 0.646 "O4'" QDM 28 QDM N1 N1 N 0 1 N N N 11.289 14.912 21.577 -5.665 1.002 0.404 N1 QDM 29 QDM C6 C6 C 0 1 N N N 10.201 14.226 21.904 -6.066 2.258 0.769 C6 QDM 30 QDM C5 C5 C 0 1 N N N 9.489 14.765 22.965 -6.816 2.993 -0.079 C5 QDM 31 QDM C5M C5M C 0 1 N N N 8.277 14.020 23.450 -7.267 4.379 0.305 C5M QDM 32 QDM C4 C4 C 0 1 N N N 9.892 15.963 23.532 -7.173 2.446 -1.335 C4 QDM 33 QDM O4 O4 O 0 1 N N N 9.243 16.584 24.541 -7.848 3.090 -2.117 O4 QDM 34 QDM N3 N3 N 0 1 N N N 11.025 16.633 23.192 -6.757 1.204 -1.657 N3 QDM 35 QDM C2 C2 C 0 1 N N N 11.671 16.057 22.155 -6.006 0.495 -0.794 C2 QDM 36 QDM O2 O2 O 0 1 N N N 12.779 16.752 21.797 -5.635 -0.622 -1.100 O2 QDM 37 QDM H1 H1 H 0 1 N N N 9.344 8.217 17.980 -0.709 -1.845 -2.502 H1 QDM 38 QDM H2 H2 H 0 1 N N N 7.759 11.738 15.228 2.785 -0.799 -2.912 H2 QDM 39 QDM H3 H3 H 0 1 N N N 11.394 12.493 14.810 5.587 -1.575 -0.375 H3 QDM 40 QDM H4 H4 H 0 1 N N N 11.347 13.974 12.828 6.869 0.092 0.913 H4 QDM 41 QDM H5 H5 H 0 1 N N N 9.447 13.860 14.232 5.584 -1.510 2.136 H5 QDM 42 QDM H6 H6 H 0 1 N N N 9.772 11.764 11.488 4.214 1.594 1.083 H6 QDM 43 QDM H8 H8 H 0 1 N N N 8.582 12.242 9.581 7.454 3.218 1.143 H8 QDM 44 QDM H9 H9 H 0 1 N N N 8.842 13.791 8.708 7.769 2.888 2.864 H9 QDM 45 QDM H10 H10 H 0 1 N N N 10.133 12.542 8.726 7.825 1.561 1.679 H10 QDM 46 QDM H11 H11 H 0 1 N N N 11.295 15.069 11.158 4.127 3.274 2.627 H11 QDM 47 QDM H12 H12 H 0 1 N N N 11.723 14.199 9.646 5.602 3.930 3.379 H12 QDM 48 QDM H13 H13 H 0 1 N N N 10.432 15.448 9.628 5.297 4.188 1.644 H13 QDM 49 QDM H14 H14 H 0 1 N N N 12.548 12.741 10.794 6.820 2.307 -0.343 H14 QDM 50 QDM H15 H15 H 0 1 N N N 12.415 10.903 9.375 5.464 4.137 -1.063 H15 QDM 51 QDM H16 H16 H 0 1 N N N 11.671 10.126 12.148 4.079 1.549 -1.455 H16 QDM 52 QDM H17 H17 H 0 1 N N N 14.157 9.906 12.493 6.734 2.192 -2.818 H17 QDM 53 QDM H18 H18 H 0 1 N N N 13.779 10.032 10.742 5.244 1.671 -3.641 H18 QDM 54 QDM H19 H19 H 0 1 N N N 14.419 11.457 11.627 5.295 3.240 -2.801 H19 QDM 55 QDM H20 H20 H 0 1 N N N 10.016 11.702 18.793 -2.882 -2.609 -0.327 H20 QDM 56 QDM H21 H21 H 0 1 N N N 11.039 11.408 20.240 -2.195 -3.295 1.165 H21 QDM 57 QDM H22 H22 H 0 1 N N N 11.925 12.932 17.731 -2.706 -1.092 2.322 H22 QDM 58 QDM H23 H23 H 0 1 N N N 13.535 11.649 19.572 -4.786 -2.963 1.173 H23 QDM 59 QDM H24 H24 H 0 1 N N N 15.075 13.316 18.961 -5.234 -3.107 3.516 H24 QDM 60 QDM H25 H25 H 0 1 N N N 12.823 12.690 21.562 -6.395 -1.312 1.054 H25 QDM 61 QDM H26 H26 H 0 1 N N N 14.120 13.834 21.075 -6.081 -0.882 2.764 H26 QDM 62 QDM H27 H27 H 0 1 N N N 12.642 15.292 20.025 -4.555 0.804 2.185 H27 QDM 63 QDM H28 H28 H 0 1 N N N 9.897 13.327 21.389 -5.785 2.659 1.732 H28 QDM 64 QDM H29 H29 H 0 1 N N N 7.821 14.566 24.289 -6.521 5.106 -0.017 H29 QDM 65 QDM H30 H30 H 0 1 N N N 7.548 13.933 22.631 -8.219 4.598 -0.177 H30 QDM 66 QDM H31 H31 H 0 1 N N N 8.574 13.015 23.785 -7.386 4.436 1.387 H31 QDM 67 QDM H32 H32 H 0 1 N N N 11.344 17.459 23.657 -6.998 0.822 -2.516 H32 QDM 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 QDM C2M N3Q SING N N 1 QDM O4Q C4Q SING N N 2 QDM C1M N3Q SING N N 3 QDM N3Q C3Q SING N N 4 QDM C4Q C3Q SING N N 5 QDM C4Q C5Q SING N N 6 QDM C3Q C2Q SING N N 7 QDM C6Q C5Q SING N N 8 QDM C5Q O5Q SING N N 9 QDM C2Q O2Q SING N N 10 QDM C2Q C1Q SING N N 11 QDM O5Q C1Q SING N N 12 QDM C1Q O3B SING N N 13 QDM O3B PB SING N N 14 QDM O2B PB DOUB N N 15 QDM PB O1B SING N N 16 QDM PB O3A SING N N 17 QDM O3A PA SING N N 18 QDM O2A PA DOUB N N 19 QDM PA O1A SING N N 20 QDM PA "O5'" SING N N 21 QDM "O5'" "C5'" SING N N 22 QDM "O3'" "C3'" SING N N 23 QDM "C4'" "C5'" SING N N 24 QDM "C4'" "C3'" SING N N 25 QDM "C4'" "O4'" SING N N 26 QDM "C3'" "C2'" SING N N 27 QDM "O4'" "C1'" SING N N 28 QDM "C1'" "C2'" SING N N 29 QDM "C1'" N1 SING N N 30 QDM N1 C6 SING N N 31 QDM N1 C2 SING N N 32 QDM O2 C2 DOUB N N 33 QDM C6 C5 DOUB N N 34 QDM C2 N3 SING N N 35 QDM C5 C5M SING N N 36 QDM C5 C4 SING N N 37 QDM N3 C4 SING N N 38 QDM C4 O4 DOUB N N 39 QDM O1A H1 SING N N 40 QDM O1B H2 SING N N 41 QDM C1Q H3 SING N N 42 QDM C2Q H4 SING N N 43 QDM O2Q H5 SING N N 44 QDM C3Q H6 SING N N 45 QDM C2M H8 SING N N 46 QDM C2M H9 SING N N 47 QDM C2M H10 SING N N 48 QDM C1M H11 SING N N 49 QDM C1M H12 SING N N 50 QDM C1M H13 SING N N 51 QDM C4Q H14 SING N N 52 QDM O4Q H15 SING N N 53 QDM C5Q H16 SING N N 54 QDM C6Q H17 SING N N 55 QDM C6Q H18 SING N N 56 QDM C6Q H19 SING N N 57 QDM "C5'" H20 SING N N 58 QDM "C5'" H21 SING N N 59 QDM "C4'" H22 SING N N 60 QDM "C3'" H23 SING N N 61 QDM "O3'" H24 SING N N 62 QDM "C2'" H25 SING N N 63 QDM "C2'" H26 SING N N 64 QDM "C1'" H27 SING N N 65 QDM C6 H28 SING N N 66 QDM C5M H29 SING N N 67 QDM C5M H30 SING N N 68 QDM C5M H31 SING N N 69 QDM N3 H32 SING N N 70 # 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 QDM SMILES ACDLabs 12.01 "O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)C(N(C)C)C3O)C)O)O)C" QDM InChI InChI 1.03 "InChI=1S/C18H31N3O14P2/c1-8-6-21(18(26)19-16(8)25)12-5-10(22)11(33-12)7-31-36(27,28)35-37(29,30)34-17-15(24)13(20(3)4)14(23)9(2)32-17/h6,9-15,17,22-24H,5,7H2,1-4H3,(H,27,28)(H,29,30)(H,19,25,26)/t9-,10+,11-,12-,13+,14-,15-,17-/m1/s1" QDM InChIKey InChI 1.03 IJJNPDQFXCRKOA-WHRNYZGVSA-N QDM SMILES_CANONICAL CACTVS 3.385 "C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@H]([C@@H]1O)N(C)C" QDM SMILES CACTVS 3.385 "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH]([CH]1O)N(C)C" QDM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)N(C)C)O" QDM SMILES "OpenEye OEToolkits" 1.7.6 "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)N(C)C)O" # 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 QDM "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,4S,5S,6R)-4-(dimethylamino)-3,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" QDM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4S,5S,6R)-4-(dimethylamino)-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site QDM "Create component" 2014-02-17 RCSB QDM "Initial release" 2014-02-26 RCSB #