data_UDZ # _chem_comp.id UDZ _chem_comp.name "[(2R,3S,4R,5R,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,4-bis(oxidanyl)oxan-2-yl]methylimino-azanylidene-azanium" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H27 N6 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2012-11-30 _chem_comp.pdbx_modified_date 2013-06-07 _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 633.374 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UDZ _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 3W1V _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 UDZ N1 N1 N 0 1 N N N -19.750 -36.809 -21.106 5.921 -0.845 0.659 N1 UDZ 1 UDZ C2 C2 C 0 1 N N N -18.617 -36.626 -20.251 5.784 -1.105 -0.654 C2 UDZ 2 UDZ O2 O2 O 0 1 N N N -17.638 -37.398 -20.320 5.225 -0.297 -1.369 O2 UDZ 3 UDZ N3 N3 N 0 1 N N N -18.631 -35.633 -19.351 6.257 -2.247 -1.186 N3 UDZ 4 UDZ C4 C4 C 0 1 N N N -19.680 -34.761 -19.211 6.879 -3.154 -0.405 C4 UDZ 5 UDZ O4 O4 O 0 1 N N N -19.687 -33.850 -18.312 7.308 -4.188 -0.886 O4 UDZ 6 UDZ C5 C5 C 0 1 N N N -20.810 -34.903 -20.084 7.030 -2.893 0.978 C5 UDZ 7 UDZ C6 C6 C 0 1 N N N -20.793 -35.940 -21.021 6.546 -1.739 1.485 C6 UDZ 8 UDZ PA PA P 0 1 N N N -23.244 -35.438 -24.416 0.295 2.155 -0.985 PA UDZ 9 UDZ PB PB P 0 1 N N N -25.513 -37.103 -24.163 -2.276 0.709 -1.271 PB UDZ 10 UDZ "C1'" "C1'" C 0 1 N N R -27.056 -34.988 -24.289 -4.689 -0.145 -0.504 "C1'" UDZ 11 UDZ "O1'" "O1'" O 0 1 N N N -26.927 -36.407 -24.492 -3.363 0.267 -0.168 "O1'" UDZ 12 UDZ O1A O1A O 0 1 N N N -22.734 -34.558 -25.525 0.682 1.817 -2.373 O1A UDZ 13 UDZ C1B C1B C 0 1 N N R -19.760 -37.864 -22.112 5.402 0.409 1.209 C1B UDZ 14 UDZ O1B O1B O 0 1 N N N -25.498 -38.507 -24.725 -2.835 1.794 -2.108 O1B UDZ 15 UDZ "C2'" "C2'" C 0 1 N N R -28.168 -34.745 -23.282 -5.641 0.217 0.639 "C2'" UDZ 16 UDZ "O2'" "O2'" O 0 1 N N N -21.111 -39.746 -21.039 7.347 1.898 1.366 "O2'" UDZ 17 UDZ O2A O2A O 0 1 N N N -23.568 -34.934 -23.041 -0.134 3.705 -0.909 O2A UDZ 18 UDZ C2B C2B C 0 1 N N R -21.035 -38.745 -22.050 6.163 1.622 0.615 C2B UDZ 19 UDZ O2B O2B O 0 1 N N N -25.217 -36.835 -22.682 -1.913 -0.554 -2.202 O2B UDZ 20 UDZ "C3'" "C3'" C 0 1 N N R -29.516 -35.285 -23.893 -5.223 -0.544 1.901 "C3'" UDZ 21 UDZ "O3'" "O3'" O 0 1 N N N -30.568 -35.069 -22.937 -6.150 -0.269 2.954 "O3'" UDZ 22 UDZ O3A O3A O 0 1 N N N -24.531 -36.165 -25.054 -0.944 1.232 -0.533 O3A UDZ 23 UDZ C3B C3B C 0 1 N N S -21.043 -39.309 -23.493 5.129 2.763 0.773 C3B UDZ 24 UDZ O3B O3B O 0 1 N N N -20.366 -40.601 -23.435 5.404 3.527 1.949 O3B UDZ 25 UDZ "C4'" "C4'" C 0 1 N N S -29.831 -34.817 -25.350 -5.220 -2.046 1.601 "C4'" UDZ 26 UDZ "O4'" "O4'" O 0 1 N N N -30.680 -35.777 -26.035 -4.764 -2.762 2.750 "O4'" UDZ 27 UDZ C4B C4B C 0 1 N N R -20.390 -38.175 -24.357 3.778 2.033 0.908 C4B UDZ 28 UDZ O4B O4B O 0 1 N N N -19.682 -37.292 -23.445 4.039 0.625 0.783 O4B UDZ 29 UDZ "C5'" "C5'" C 0 1 N N R -28.549 -34.809 -26.227 -4.285 -2.321 0.420 "C5'" UDZ 30 UDZ "O5'" "O5'" O 0 1 N N N -27.367 -34.354 -25.535 -4.711 -1.559 -0.711 "O5'" UDZ 31 UDZ C5B C5B C 0 1 N N N -21.378 -37.306 -25.117 2.829 2.488 -0.202 C5B UDZ 32 UDZ O5B O5B O 0 1 N N N -22.271 -36.751 -24.142 1.544 1.895 -0.002 O5B UDZ 33 UDZ "C6'" "C6'" C 0 1 N N N -28.713 -34.163 -27.626 -4.322 -3.811 0.075 "C6'" UDZ 34 UDZ "C7'" "C7'" C 0 1 N N N -28.292 -35.150 -20.792 -6.333 2.505 0.167 "C7'" UDZ 35 UDZ "O7'" "O7'" O 0 1 N N N -28.271 -35.972 -19.879 -7.068 2.074 -0.695 "O7'" UDZ 36 UDZ "C8'" "C8'" C 0 1 N N N -28.883 -33.797 -20.559 -6.266 3.988 0.428 "C8'" UDZ 37 UDZ "N2'" "N2'" N 0 1 N N N -27.790 -35.401 -22.021 -5.576 1.658 0.893 "N2'" UDZ 38 UDZ N41 N41 N 0 1 N N N -26.737 -31.555 -26.551 -1.673 -5.551 -0.591 N41 UDZ 39 UDZ N40 N40 N 1 1 N N N -27.692 -32.037 -27.040 -2.507 -4.823 -0.783 N40 UDZ 40 UDZ "N6'" "N6'" N 0 1 N N N -28.719 -32.706 -27.507 -3.340 -4.094 -0.975 "N6'" UDZ 41 UDZ H1 H1 H 0 1 N N N -17.838 -35.523 -18.752 6.150 -2.419 -2.134 H1 UDZ 42 UDZ H2 H2 H 0 1 N N N -21.650 -34.227 -20.019 7.525 -3.608 1.619 H2 UDZ 43 UDZ H3 H3 H 0 1 N N N -21.629 -36.054 -21.695 6.653 -1.523 2.538 H3 UDZ 44 UDZ H4 H4 H 0 1 N N N -26.117 -34.581 -23.885 -5.007 0.361 -1.416 H4 UDZ 45 UDZ H5 H5 H 0 1 N N N -18.891 -38.519 -21.951 5.470 0.408 2.297 H5 UDZ 46 UDZ H6 H6 H 0 1 N N N -28.272 -33.662 -23.119 -6.659 -0.059 0.366 H6 UDZ 47 UDZ H7 H7 H 0 1 N N N -21.102 -39.334 -20.183 7.857 2.649 1.033 H7 UDZ 48 UDZ H8 H8 H 0 1 N N N -23.401 -34.000 -22.998 -0.400 3.996 -0.026 H8 UDZ 49 UDZ H9 H9 H 0 1 N N N -21.898 -38.070 -21.954 6.401 1.455 -0.436 H9 UDZ 50 UDZ H10 H10 H 0 1 N N N -25.040 -37.657 -22.240 -1.541 -1.304 -1.719 H10 UDZ 51 UDZ H11 H11 H 0 1 N N N -29.379 -36.374 -23.965 -4.224 -0.229 2.203 H11 UDZ 52 UDZ H12 H12 H 0 1 N N N -30.290 -35.382 -22.084 -5.946 -0.720 3.785 H12 UDZ 53 UDZ H13 H13 H 0 1 N N N -22.086 -39.443 -23.817 5.132 3.405 -0.107 H13 UDZ 54 UDZ H14 H14 H 0 1 N N N -20.862 -41.194 -22.883 6.268 3.961 1.943 H14 UDZ 55 UDZ H15 H15 H 0 1 N N N -30.285 -33.815 -25.334 -6.230 -2.369 1.348 H15 UDZ 56 UDZ H16 H16 H 0 1 N N N -31.505 -35.858 -25.571 -4.736 -3.721 2.631 H16 UDZ 57 UDZ H17 H17 H 0 1 N N N -19.686 -38.633 -25.067 3.339 2.244 1.883 H17 UDZ 58 UDZ H18 H18 H 0 1 N N N -28.365 -35.872 -26.442 -3.267 -2.035 0.689 H18 UDZ 59 UDZ H19 H19 H 0 1 N N N -20.847 -36.501 -25.646 2.736 3.573 -0.179 H19 UDZ 60 UDZ H20 H20 H 0 1 N N N -21.939 -37.914 -25.842 3.225 2.177 -1.169 H20 UDZ 61 UDZ H21 H21 H 0 1 N N N -29.662 -34.496 -28.072 -4.083 -4.396 0.964 H21 UDZ 62 UDZ H22 H22 H 0 1 N N N -27.877 -34.472 -28.270 -5.318 -4.077 -0.277 H22 UDZ 63 UDZ H23 H23 H 0 1 N N N -29.242 -33.727 -19.522 -7.007 4.258 1.180 H23 UDZ 64 UDZ H24 H24 H 0 1 N N N -28.117 -33.027 -20.734 -5.271 4.249 0.788 H24 UDZ 65 UDZ H25 H25 H 0 1 N N N -29.725 -33.641 -21.250 -6.471 4.529 -0.496 H25 UDZ 66 UDZ H26 H26 H 0 1 N N N -27.086 -36.109 -22.080 -4.988 2.003 1.582 H26 UDZ 67 UDZ H27 H27 H 0 1 N N N -26.255 -32.199 -25.957 -0.830 -5.239 -0.226 H27 UDZ 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 UDZ "C6'" "N6'" SING N N 1 UDZ "C6'" "C5'" SING N N 2 UDZ "N6'" N40 DOUB N N 3 UDZ N40 N41 DOUB N N 4 UDZ "C5'" "O5'" SING N N 5 UDZ "C5'" "C4'" SING N N 6 UDZ "O4'" "C4'" SING N N 7 UDZ "O5'" "C1'" SING N N 8 UDZ O1A PA DOUB N N 9 UDZ "C4'" "C3'" SING N N 10 UDZ C5B C4B SING N N 11 UDZ C5B O5B SING N N 12 UDZ O3A PA SING N N 13 UDZ O3A PB SING N N 14 UDZ O1B PB DOUB N N 15 UDZ "O1'" "C1'" SING N N 16 UDZ "O1'" PB SING N N 17 UDZ PA O5B SING N N 18 UDZ PA O2A SING N N 19 UDZ C4B C3B SING N N 20 UDZ C4B O4B SING N N 21 UDZ "C1'" "C2'" SING N N 22 UDZ PB O2B SING N N 23 UDZ "C3'" "C2'" SING N N 24 UDZ "C3'" "O3'" SING N N 25 UDZ C3B O3B SING N N 26 UDZ C3B C2B SING N N 27 UDZ O4B C1B SING N N 28 UDZ "C2'" "N2'" SING N N 29 UDZ C1B C2B SING N N 30 UDZ C1B N1 SING N N 31 UDZ C2B "O2'" SING N N 32 UDZ "N2'" "C7'" SING N N 33 UDZ N1 C6 SING N N 34 UDZ N1 C2 SING N N 35 UDZ C6 C5 DOUB N N 36 UDZ "C7'" "C8'" SING N N 37 UDZ "C7'" "O7'" DOUB N N 38 UDZ O2 C2 DOUB N N 39 UDZ C2 N3 SING N N 40 UDZ C5 C4 SING N N 41 UDZ N3 C4 SING N N 42 UDZ C4 O4 DOUB N N 43 UDZ N3 H1 SING N N 44 UDZ C5 H2 SING N N 45 UDZ C6 H3 SING N N 46 UDZ "C1'" H4 SING N N 47 UDZ C1B H5 SING N N 48 UDZ "C2'" H6 SING N N 49 UDZ "O2'" H7 SING N N 50 UDZ O2A H8 SING N N 51 UDZ C2B H9 SING N N 52 UDZ O2B H10 SING N N 53 UDZ "C3'" H11 SING N N 54 UDZ "O3'" H12 SING N N 55 UDZ C3B H13 SING N N 56 UDZ O3B H14 SING N N 57 UDZ "C4'" H15 SING N N 58 UDZ "O4'" H16 SING N N 59 UDZ C4B H17 SING N N 60 UDZ "C5'" H18 SING N N 61 UDZ C5B H19 SING N N 62 UDZ C5B H20 SING N N 63 UDZ "C6'" H21 SING N N 64 UDZ "C6'" H22 SING N N 65 UDZ "C8'" H23 SING N N 66 UDZ "C8'" H24 SING N N 67 UDZ "C8'" H25 SING N N 68 UDZ "N2'" H26 SING N N 69 UDZ N41 H27 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 UDZ SMILES ACDLabs 12.01 "O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3NC(=O)C)C/N=[N+]=[N@H])O)O" UDZ InChI InChI 1.03 ;InChI=1S/C17H26N6O16P2/c1-6(24)20-10-13(28)11(26)7(4-19-22-18)37-16(10)38-41(33,34)39-40(31,32)35-5-8-12(27)14(29)15(36-8)23-3-2-9(25)21-17(23)30/h2-3,7-8,10-16,18,26-29H,4-5H2,1H3,(H3-,20,21,24,25,30,31,32,33,34)/p+1/t7-,8-,10-,11-,12-,13-,14-,15-,16-/m1/s1 ; UDZ InChIKey InChI 1.03 JRORMXITLCSMOP-CFRASDGPSA-O UDZ SMILES_CANONICAL CACTVS 3.370 "CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CN=[N+]=N)O[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O" UDZ SMILES CACTVS 3.370 "CC(=O)N[CH]1[CH](O)[CH](O)[CH](CN=[N+]=N)O[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O" UDZ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CN=[N+]=N)O)O" UDZ SMILES "OpenEye OEToolkits" 1.7.6 "CC(=O)NC1C(C(C(OC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CN=[N+]=N)O)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 UDZ "SYSTEMATIC NAME" ACDLabs 12.01 ;1-{[(2R,3S,4R,5R,6R)-5-(acetylamino)-6-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4-dihydroxytetrahydro-2H-pyran-2-yl]methyl}triaza-1,2-dien-2-ium (non-preferred name) ; UDZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,4-bis(oxidanyl)oxan-2-yl]methylimino-azanylidene-azanium" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site UDZ "Create component" 2012-11-30 PDBJ UDZ "Initial release" 2013-06-12 RCSB #