data_QCK # _chem_comp.id QCK _chem_comp.name "(4-methyltriazole)-Thymidine-5'-monophosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H18 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-06-05 _chem_comp.pdbx_modified_date 2021-01-22 _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 403.284 _chem_comp.one_letter_code T _chem_comp.three_letter_code QCK _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 6Z8W _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 QCK N1 N1 N 0 1 N N N 61.394 -41.134 31.688 -1.023 1.180 -0.071 N1 QCK 1 QCK C4 C1 C 0 1 N N N 61.195 -40.185 34.261 -3.285 0.884 1.405 C4 QCK 2 QCK C5 C2 C 0 1 N N N 62.456 -40.445 33.718 -2.061 1.208 2.038 C5 QCK 3 QCK C6 C3 C 0 1 N N N 62.539 -40.933 32.407 -0.949 1.351 1.285 C6 QCK 4 QCK C7 C4 C 0 1 N N N 63.688 -40.180 34.546 -1.999 1.393 3.532 C7 QCK 5 QCK C8 C5 C 0 1 Y N N 58.973 -42.580 35.082 -5.390 -1.904 0.203 C8 QCK 6 QCK C1 C6 C 0 1 N N N 58.620 -40.165 34.152 -4.576 0.386 -0.600 C1 QCK 7 QCK C2 C7 C 0 1 N N N 60.090 -40.893 32.255 -2.192 0.871 -0.660 C2 QCK 8 QCK C9 C8 C 0 1 Y N N 58.184 -41.412 34.898 -4.723 -1.112 -0.669 C9 QCK 9 QCK O2 O1 O 0 1 N N N 58.998 -41.083 31.666 -2.234 0.723 -1.866 O2 QCK 10 QCK "C1'" C9 C 0 1 N N R 61.466 -41.638 30.302 0.182 1.340 -0.889 "C1'" QCK 11 QCK "C2'" C10 C 0 1 N N N 62.348 -40.847 29.342 0.729 2.780 -0.764 "C2'" QCK 12 QCK "C3'" C11 C 0 1 N N S 63.144 -41.906 28.634 2.263 2.601 -0.778 "C3'" QCK 13 QCK "O3'" O2 O 0 1 N N N 62.847 -41.867 27.229 2.837 3.279 -1.898 "O3'" QCK 14 QCK "C4'" C12 C 0 1 N N R 62.687 -43.255 29.199 2.462 1.075 -0.909 "C4'" QCK 15 QCK "C5'" C13 C 0 1 N N N 63.857 -44.203 29.445 3.663 0.621 -0.076 "C5'" QCK 16 QCK "O5'" O3 O 0 1 N N N 64.724 -43.659 30.395 3.901 -0.770 -0.302 "O5'" QCK 17 QCK P P1 P 0 1 N N N 65.977 -44.503 30.952 5.091 -1.584 0.414 P QCK 18 QCK OP2 O4 O 0 1 N N N 66.363 -45.724 29.977 6.510 -1.008 -0.084 OP2 QCK 19 QCK OP1 O5 O 0 1 N N N 65.754 -44.985 32.471 4.982 -1.428 1.881 OP1 QCK 20 QCK "O4'" O6 O 0 1 N N N 62.123 -42.890 30.443 1.244 0.498 -0.391 "O4'" QCK 21 QCK O4 O7 O 0 1 N N N 61.082 -39.780 35.425 -4.301 0.750 2.063 O4 QCK 22 QCK N3 N2 N 0 1 N N N 59.975 -40.414 33.560 -3.315 0.723 0.066 N3 QCK 23 QCK N10 N3 N 0 1 Y N N 56.971 -41.604 35.509 -4.214 -1.936 -1.614 N10 QCK 24 QCK N11 N4 N 0 1 Y N N 56.981 -42.912 36.065 -4.557 -3.142 -1.324 N11 QCK 25 QCK N12 N5 N 0 1 Y N N 58.263 -43.480 35.784 -5.259 -3.157 -0.246 N12 QCK 26 QCK H1 H1 H 0 1 N N N 63.502 -41.149 31.967 -0.007 1.598 1.750 H1 QCK 27 QCK H2 H2 H 0 1 N N N 63.391 -39.804 35.536 -2.991 1.238 3.958 H2 QCK 28 QCK H3 H3 H 0 1 N N N 64.258 -41.113 34.665 -1.303 0.671 3.959 H3 QCK 29 QCK H4 H4 H 0 1 N N N 64.314 -39.430 34.041 -1.660 2.403 3.760 H4 QCK 30 QCK H5 H5 H 0 1 N N N 59.980 -42.721 34.717 -5.920 -1.587 1.089 H5 QCK 31 QCK H6 H6 H 0 1 N N N 58.670 -39.315 34.848 -4.575 0.798 -1.609 H6 QCK 32 QCK H7 H7 H 0 1 N N N 57.900 -39.941 33.351 -5.408 0.808 -0.036 H7 QCK 33 QCK H8 H8 H 0 1 N N N 60.458 -41.756 29.878 -0.033 1.103 -1.931 H8 QCK 34 QCK H9 H9 H 0 1 N N N 63.009 -40.161 29.892 0.407 3.385 -1.612 H9 QCK 35 QCK H10 H10 H 0 1 N N N 61.736 -40.274 28.629 0.403 3.232 0.172 H10 QCK 36 QCK H11 H11 H 0 1 N N N 64.219 -41.766 28.820 2.698 2.964 0.153 H11 QCK 37 QCK H12 H12 H 0 1 N N N 63.127 -41.034 26.869 2.740 4.241 -1.867 H12 QCK 38 QCK H13 H13 H 0 1 N N N 61.949 -43.721 28.529 2.600 0.799 -1.954 H13 QCK 39 QCK H14 H14 H 0 1 N N N 63.474 -45.167 29.812 4.544 1.192 -0.368 H14 QCK 40 QCK H15 H15 H 0 1 N N N 64.402 -44.360 28.503 3.456 0.787 0.981 H15 QCK 41 QCK H16 H16 H 0 1 N N N 66.393 -46.532 30.477 6.650 -1.079 -1.038 H16 QCK 42 QCK H18 H18 H 0 1 N N N 56.219 -40.946 35.555 -3.684 -1.664 -2.379 H18 QCK 43 QCK OP3 OP3 O 0 1 N Y N 67.175 -43.442 30.930 4.981 -3.144 0.031 OP3 QCK 44 QCK H17 H17 H 0 1 N N N 67.504 -43.317 31.812 5.668 -3.696 0.428 H17 QCK 45 # # 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 QCK "O3'" "C3'" SING N N 1 QCK "C3'" "C4'" SING N N 2 QCK "C3'" "C2'" SING N N 3 QCK "C4'" "C5'" SING N N 4 QCK "C4'" "O4'" SING N N 5 QCK "C2'" "C1'" SING N N 6 QCK "C5'" "O5'" SING N N 7 QCK OP2 P SING N N 8 QCK "C1'" "O4'" SING N N 9 QCK "C1'" N1 SING N N 10 QCK "O5'" P SING N N 11 QCK P OP1 DOUB N N 12 QCK O2 C2 DOUB N N 13 QCK N1 C2 SING N N 14 QCK N1 C6 SING N N 15 QCK C2 N3 SING N N 16 QCK C6 C5 DOUB N N 17 QCK N3 C1 SING N N 18 QCK N3 C4 SING N N 19 QCK C5 C4 SING N N 20 QCK C5 C7 SING N N 21 QCK C1 C9 SING N N 22 QCK C4 O4 DOUB N N 23 QCK C9 C8 DOUB Y N 24 QCK C9 N10 SING Y N 25 QCK C8 N12 SING Y N 26 QCK N10 N11 SING Y N 27 QCK N12 N11 DOUB Y N 28 QCK C6 H1 SING N N 29 QCK C7 H2 SING N N 30 QCK C7 H3 SING N N 31 QCK C7 H4 SING N N 32 QCK C8 H5 SING N N 33 QCK C1 H6 SING N N 34 QCK C1 H7 SING N N 35 QCK "C1'" H8 SING N N 36 QCK "C2'" H9 SING N N 37 QCK "C2'" H10 SING N N 38 QCK "C3'" H11 SING N N 39 QCK "O3'" H12 SING N N 40 QCK "C4'" H13 SING N N 41 QCK "C5'" H14 SING N N 42 QCK "C5'" H15 SING N N 43 QCK OP2 H16 SING N N 44 QCK N10 H18 SING N N 45 QCK P OP3 SING N N 46 QCK OP3 H17 SING N N 47 # # 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 QCK InChI InChI 1.03 "InChI=1S/C13H18N5O8P/c1-7-4-17(11-2-9(19)10(26-11)6-25-27(22,23)24)13(21)18(12(7)20)5-8-3-14-16-15-8/h3-4,9-11,19H,2,5-6H2,1H3,(H,14,15,16)(H2,22,23,24)/t9-,10+,11+/m0/s1" QCK InChIKey InChI 1.03 CSMLWNXTBCGKPQ-HBNTYKKESA-N QCK SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N(Cc3[nH]nnc3)C1=O" QCK SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N(Cc3[nH]nnc3)C1=O" QCK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N(C1=O)Cc2cnn[nH]2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O" QCK SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N(C1=O)Cc2cnn[nH]2)C3CC(C(O3)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id QCK _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)-3-(1~{H}-1,2,3-triazol-5-ylmethyl)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen 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 QCK "Create component" 2020-06-05 PDBE QCK "Other modification" 2020-07-24 PDBE QCK "Initial release" 2021-01-27 RCSB ##