data_QCE # _chem_comp.id QCE _chem_comp.name "N3-(N-(1-amino-4-methyl-1-oxopentan-2-yl)-2-amino-2-oxo-ethyl)-2'-deoxythymidine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H20 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[(2~{R},3~{S},5~{R})-5-[5-methyl-3-[2-(methylamino)-2-oxidanylidene-ethyl]-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-06-04 _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 377.287 _chem_comp.one_letter_code ? _chem_comp.three_letter_code QCE _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 6Z8X _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 QCE N N1 N 0 1 N N N -30.202 30.481 15.111 -6.226 -0.426 1.352 N QCE 1 QCE O4 O1 O 0 1 N N N -29.095 33.618 14.033 -3.678 2.507 -0.627 O4 QCE 2 QCE C4 C1 C 0 1 N N N -28.827 33.386 12.831 -2.773 1.704 -0.492 C4 QCE 3 QCE N3 N2 N 0 1 N N N -29.397 32.267 12.164 -2.844 0.753 0.461 N3 QCE 4 QCE C2 C2 C 0 1 N N N -29.067 32.047 10.804 -1.842 -0.134 0.611 C2 QCE 5 QCE O2 O2 O 0 1 N N N -29.553 31.071 10.186 -1.921 -0.987 1.474 O2 QCE 6 QCE C5 C3 C 0 1 N N N -27.960 34.230 12.141 -1.638 1.757 -1.337 C5 QCE 7 QCE C7 C4 C 0 1 N N N -27.334 35.424 12.821 -1.537 2.807 -2.413 C7 QCE 8 QCE C6 C5 C 0 1 N N N -27.654 33.979 10.805 -0.648 0.855 -1.165 C6 QCE 9 QCE N1 N3 N 0 1 N N N -28.181 32.934 10.145 -0.757 -0.091 -0.183 N1 QCE 10 QCE "C1'" C6 C 0 1 N N R -27.839 32.703 8.737 0.317 -1.070 0.004 "C1'" QCE 11 QCE "O4'" O3 O 0 1 N N N -26.423 32.584 8.574 1.591 -0.400 0.134 "O4'" QCE 12 QCE "C2'" C7 C 0 1 N N N -28.320 33.864 7.875 0.461 -1.956 -1.253 "C2'" QCE 13 QCE "C3'" C8 C 0 1 N N S -27.083 34.373 7.165 1.985 -2.180 -1.382 "C3'" QCE 14 QCE "O3'" O4 O 0 1 N N N -27.319 34.438 5.758 2.297 -3.571 -1.281 "O3'" QCE 15 QCE "C4'" C9 C 0 1 N N R -25.978 33.373 7.469 2.581 -1.402 -0.185 "C4'" QCE 16 QCE "C5'" C10 C 0 1 N N N -24.674 34.076 7.815 3.900 -0.738 -0.586 "C5'" QCE 17 QCE "O5'" O5 O 0 1 N N N -24.834 34.772 9.048 4.492 -0.124 0.561 "O5'" QCE 18 QCE P P1 P 0 1 N N N -23.613 35.589 9.702 5.892 0.669 0.507 P QCE 19 QCE OP1 O6 O 0 1 N N N -23.600 35.333 11.290 5.414 2.170 0.170 OP1 QCE 20 QCE OP2 O7 O 0 1 N N N -22.215 35.125 9.049 6.274 0.781 2.067 OP2 QCE 21 QCE "CA'" C11 C 0 1 N N N -29.646 31.130 16.287 -7.236 -1.299 0.749 "CA'" QCE 22 QCE C1 C12 C 0 1 N N N -29.622 30.524 13.908 -5.055 -0.213 0.718 C1 QCE 23 QCE O21 O8 O 0 1 N N N -28.590 29.929 13.636 -4.839 -0.744 -0.350 O21 QCE 24 QCE C3 C13 C 0 1 N N N -30.323 31.349 12.852 -4.016 0.685 1.338 C3 QCE 25 QCE H1 H1 H 0 1 N N N -31.061 29.978 15.207 -6.400 0.001 2.205 H1 QCE 26 QCE H2 H2 H 0 1 N N N -27.679 35.475 13.864 -2.427 3.436 -2.393 H2 QCE 27 QCE H3 H3 H 0 1 N N N -26.239 35.324 12.802 -0.653 3.421 -2.239 H3 QCE 28 QCE H4 H4 H 0 1 N N N -27.628 36.343 12.292 -1.456 2.323 -3.386 H4 QCE 29 QCE H5 H5 H 0 1 N N N -26.976 34.641 10.287 0.225 0.880 -1.800 H5 QCE 30 QCE H6 H6 H 0 1 N N N -28.332 31.783 8.390 0.121 -1.685 0.882 H6 QCE 31 QCE H7 H7 H 0 1 N N N -28.757 34.655 8.503 -0.054 -2.906 -1.112 H7 QCE 32 QCE H8 H8 H 0 1 N N N -29.068 33.519 7.146 0.073 -1.439 -2.131 H8 QCE 33 QCE H9 H9 H 0 1 N N N -26.807 35.360 7.563 2.352 -1.772 -2.324 H9 QCE 34 QCE H10 H10 H 0 1 N N N -28.010 35.065 5.581 1.947 -4.106 -2.006 H10 QCE 35 QCE H11 H11 H 0 1 N N N -25.818 32.737 6.586 2.735 -2.069 0.663 H11 QCE 36 QCE H12 H12 H 0 1 N N N -23.869 33.333 7.913 4.579 -1.491 -0.985 H12 QCE 37 QCE H13 H13 H 0 1 N N N -24.418 34.791 7.019 3.710 0.020 -1.346 H13 QCE 38 QCE H14 H14 H 0 1 N N N -22.881 35.813 11.683 6.138 2.806 0.097 H14 QCE 39 QCE H15 H15 H 0 1 N N N -21.503 35.615 9.443 7.108 1.240 2.236 H15 QCE 40 QCE H16 H16 H 0 1 N N N -30.303 30.951 17.151 -6.823 -2.300 0.623 H16 QCE 41 QCE H17 H17 H 0 1 N N N -28.647 30.719 16.495 -8.110 -1.346 1.399 H17 QCE 42 QCE H18 H18 H 0 1 N N N -29.566 32.212 16.105 -7.528 -0.901 -0.222 H18 QCE 43 QCE H19 H19 H 0 1 N N N -31.117 31.940 13.332 -3.721 0.284 2.308 H19 QCE 44 QCE H20 H20 H 0 1 N N N -30.768 30.671 12.109 -4.430 1.684 1.469 H20 QCE 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 QCE "O3'" "C3'" SING N N 1 QCE "C3'" "C4'" SING N N 2 QCE "C3'" "C2'" SING N N 3 QCE "C4'" "C5'" SING N N 4 QCE "C4'" "O4'" SING N N 5 QCE "C5'" "O5'" SING N N 6 QCE "C2'" "C1'" SING N N 7 QCE "O4'" "C1'" SING N N 8 QCE "C1'" N1 SING N N 9 QCE "O5'" P SING N N 10 QCE OP2 P SING N N 11 QCE P OP1 SING N N 12 QCE N1 C2 SING N N 13 QCE N1 C6 SING N N 14 QCE O2 C2 DOUB N N 15 QCE C2 N3 SING N N 16 QCE C6 C5 DOUB N N 17 QCE C5 C7 SING N N 18 QCE C5 C4 SING N N 19 QCE N3 C4 SING N N 20 QCE N3 C3 SING N N 21 QCE C4 O4 DOUB N N 22 QCE C3 C1 SING N N 23 QCE O21 C1 DOUB N N 24 QCE C1 N SING N N 25 QCE N "CA'" SING N N 26 QCE N H1 SING N N 27 QCE C7 H2 SING N N 28 QCE C7 H3 SING N N 29 QCE C7 H4 SING N N 30 QCE C6 H5 SING N N 31 QCE "C1'" H6 SING N N 32 QCE "C2'" H7 SING N N 33 QCE "C2'" H8 SING N N 34 QCE "C3'" H9 SING N N 35 QCE "O3'" H10 SING N N 36 QCE "C4'" H11 SING N N 37 QCE "C5'" H12 SING N N 38 QCE "C5'" H13 SING N N 39 QCE OP1 H14 SING N N 40 QCE OP2 H15 SING N N 41 QCE "CA'" H16 SING N N 42 QCE "CA'" H17 SING N N 43 QCE "CA'" H18 SING N N 44 QCE C3 H19 SING N N 45 QCE C3 H20 SING N N 46 # # 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 QCE InChI InChI 1.03 "InChI=1S/C13H20N3O8P/c1-7-4-15(13(20)16(12(7)19)5-10(18)14-2)11-3-8(17)9(24-11)6-23-25(21)22/h4,8-9,11,17,21-22H,3,5-6H2,1-2H3,(H,14,18)/t8-,9+,11+/m0/s1" QCE InChIKey InChI 1.03 IFRBNITUSZIOEY-IQJOONFLSA-N QCE SMILES_CANONICAL CACTVS 3.385 "CNC(=O)CN1C(=O)N(C=C(C)C1=O)[C@H]2C[C@H](O)[C@@H](COP(O)O)O2" QCE SMILES CACTVS 3.385 "CNC(=O)CN1C(=O)N(C=C(C)C1=O)[CH]2C[CH](O)[CH](COP(O)O)O2" QCE SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N(C1=O)CC(=O)NC)[C@H]2C[C@@H]([C@H](O2)COP(O)O)O" QCE SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)N(C1=O)CC(=O)NC)C2CC(C(O2)COP(O)O)O" # _pdbx_chem_comp_identifier.comp_id QCE _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-3-[2-(methylamino)-2-oxidanylidene-ethyl]-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id QCE _pdbx_chem_comp_synonyms.name "[(2~{R},3~{S},5~{R})-5-[5-methyl-3-[2-(methylamino)-2-oxidanylidene-ethyl]-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site QCE "Create component" 2020-06-04 PDBE QCE "Modify synonyms" 2020-10-23 PDBE QCE "Initial release" 2021-01-27 RCSB ##