data_A1EOD # _chem_comp.id A1EOD _chem_comp.name "[[(2R,3S,5R)-5-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H18 N3 O14 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2'-deoxy-5-hydroxymethyl-CTP" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-04-01 _chem_comp.pdbx_modified_date 2026-02-06 _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 497.183 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1EOD _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 9U7Z _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBC _chem_comp.pdbx_pcm ? # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 A1EOD C10 C1 C 0 1 N N N N N N -34.259 -9.939 18.833 -4.291 2.217 -0.438 C10 A1EOD 1 A1EOD C13 C2 C 0 1 N N R N N N -33.045 -11.855 19.182 -1.880 2.297 -0.773 C13 A1EOD 2 A1EOD C15 C3 C 0 1 N N N N N N -31.672 -12.256 19.564 -0.646 2.698 0.038 C15 A1EOD 3 A1EOD C02 C4 C 0 1 N N N N N N -34.174 -8.798 21.765 -4.241 -0.329 1.201 C02 A1EOD 4 A1EOD C04 C5 C 0 1 N N N N N N -35.902 -7.773 23.326 -5.546 -2.235 1.223 C04 A1EOD 5 A1EOD C06 C6 C 0 1 N N N N N N -36.944 -8.668 22.757 -5.668 -2.166 -0.180 C06 A1EOD 6 A1EOD C07 C7 C 0 1 N N N N N N -36.577 -9.631 21.677 -5.055 -1.156 -0.842 C07 A1EOD 7 A1EOD C09 C8 C 0 1 N N R N N N -34.866 -10.645 20.121 -3.671 0.862 -0.843 C09 A1EOD 8 A1EOD C11 C9 C 0 1 N N S N N N -33.005 -10.799 18.426 -3.086 3.183 -0.391 C11 A1EOD 9 A1EOD C29 C10 C 0 1 N N N N N N -38.384 -8.596 23.267 -6.467 -3.200 -0.930 C29 A1EOD 10 A1EOD N03 N1 N 0 1 N N N N N N -34.540 -7.840 22.838 -4.838 -1.316 1.866 N03 A1EOD 11 A1EOD N05 N2 N 0 1 N N N N N N -36.246 -6.835 24.379 -6.158 -3.250 1.921 N05 A1EOD 12 A1EOD N08 N3 N 0 1 N N N N N N -35.210 -9.693 21.179 -4.338 -0.235 -0.138 N08 A1EOD 13 A1EOD O01 O1 O 0 1 N N N N N N -33.059 -8.844 21.372 -3.600 0.508 1.815 O01 A1EOD 14 A1EOD O12 O2 O 0 1 N N N N N N -33.079 -11.212 17.002 -3.253 4.238 -1.341 O12 A1EOD 15 A1EOD O14 O3 O 0 1 N N N N N N -33.931 -11.423 20.548 -2.288 0.953 -0.436 O14 A1EOD 16 A1EOD O16 O4 O 0 1 N N N N N N -30.974 -12.580 18.400 0.467 1.896 -0.360 O16 A1EOD 17 A1EOD O18 O5 O 0 1 N N N N N N -29.659 -14.286 16.972 1.840 1.905 1.758 O18 A1EOD 18 A1EOD O19 O6 O 0 1 N N N N N N -31.336 -15.122 18.576 2.533 3.497 -0.074 O19 A1EOD 19 A1EOD O20 O7 O 0 1 N N N N N N -29.130 -14.149 19.502 2.901 0.904 -0.301 O20 A1EOD 20 A1EOD O22 O8 O 0 1 N N N N N N -27.597 -16.072 18.739 4.207 -0.048 1.638 O22 A1EOD 21 A1EOD O23 O9 O 0 1 N N N N N N -29.324 -16.551 20.437 5.494 1.283 -0.079 O23 A1EOD 22 A1EOD O24 O10 O 0 1 N N N N N N -27.263 -15.159 21.123 4.557 -1.113 -0.624 O24 A1EOD 23 A1EOD O26 O11 O 0 1 N N N N N N -24.962 -14.538 22.111 7.018 -2.037 -0.655 O26 A1EOD 24 A1EOD O27 O12 O 0 1 N N N N N N -25.362 -14.139 19.709 5.333 -2.843 1.042 O27 A1EOD 25 A1EOD O28 O13 O 0 1 N N N N N N -25.110 -16.444 20.550 5.019 -3.598 -1.345 O28 A1EOD 26 A1EOD O30 O14 O 0 1 N N N N N N -39.070 -7.640 22.497 -6.433 -2.905 -2.328 O30 A1EOD 27 A1EOD P17 P1 P 0 1 N N N N N N -30.283 -14.068 18.330 1.933 2.048 0.288 P17 A1EOD 28 A1EOD P21 P2 P 0 1 N N N N N N -28.339 -15.524 19.934 4.288 0.250 0.190 P21 A1EOD 29 A1EOD P25 P3 P 0 1 N N N N N N -25.639 -15.066 20.869 5.478 -2.407 -0.365 P25 A1EOD 30 A1EOD H102 H1 H 0 0 N N N N N N -33.957 -8.908 19.068 -5.014 2.545 -1.186 H102 A1EOD 31 A1EOD H101 H2 H 0 0 N N N N N N -34.997 -9.928 18.018 -4.763 2.144 0.541 H101 A1EOD 32 A1EOD H131 H3 H 0 0 N N N N N N -33.564 -12.701 18.707 -1.673 2.374 -1.840 H131 A1EOD 33 A1EOD H151 H4 H 0 0 N N N N N N -31.711 -13.130 20.231 -0.420 3.749 -0.141 H151 A1EOD 34 A1EOD H152 H5 H 0 0 N N N N N N -31.171 -11.424 20.080 -0.844 2.545 1.099 H152 A1EOD 35 A1EOD H071 H6 H 0 0 N N N N N N -37.330 -10.285 21.263 -5.133 -1.082 -1.917 H071 A1EOD 36 A1EOD H091 H7 H 0 0 N N N N N N -35.766 -11.198 19.814 -3.740 0.720 -1.921 H091 A1EOD 37 A1EOD H111 H8 H 0 0 N N N N N N -32.100 -10.196 18.590 -2.960 3.588 0.613 H111 A1EOD 38 A1EOD H291 H9 H 0 0 N N N N N N -38.391 -8.297 24.326 -6.038 -4.187 -0.757 H291 A1EOD 39 A1EOD H292 H10 H 0 0 N N N N N N -38.868 -9.578 23.160 -7.499 -3.185 -0.581 H292 A1EOD 40 A1EOD H051 H11 H 0 0 N N N N N N -35.543 -6.237 24.765 -6.676 -3.920 1.449 H051 A1EOD 41 A1EOD H052 H12 H 0 0 N N N N N N -37.186 -6.786 24.718 -6.073 -3.295 2.887 H052 A1EOD 42 A1EOD H121 H13 H 0 0 N N N N N N -32.313 -11.728 16.781 -4.031 4.790 -1.183 H121 A1EOD 43 A1EOD H1 H14 H 0 1 N N N N N N -31.386 -15.702 17.825 2.622 3.660 -1.023 H1 A1EOD 44 A1EOD H2 H15 H 0 1 N N N N N N -29.273 -17.331 19.897 5.605 1.523 -1.009 H2 A1EOD 45 A1EOD H3 H16 H 0 1 N N N N N N -24.503 -13.733 21.904 7.188 -1.742 -1.561 H3 A1EOD 46 A1EOD H4 H17 H 0 1 N N N N N N -24.714 -16.440 19.687 5.532 -4.412 -1.244 H4 A1EOD 47 A1EOD H301 H18 H 0 0 N N N N N N -39.969 -7.578 22.796 -6.929 -3.531 -2.874 H301 A1EOD 48 # 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 A1EOD O18 P17 DOUB N N 1 A1EOD O12 C11 SING N N 2 A1EOD P17 O16 SING N N 3 A1EOD P17 O19 SING N N 4 A1EOD P17 O20 SING N N 5 A1EOD O16 C15 SING N N 6 A1EOD C11 C10 SING N N 7 A1EOD C11 C13 SING N N 8 A1EOD O22 P21 DOUB N N 9 A1EOD C10 C09 SING N N 10 A1EOD C13 C15 SING N N 11 A1EOD C13 O14 SING N N 12 A1EOD O20 P21 SING N N 13 A1EOD O27 P25 DOUB N N 14 A1EOD P21 O23 SING N N 15 A1EOD P21 O24 SING N N 16 A1EOD C09 O14 SING N N 17 A1EOD C09 N08 SING N N 18 A1EOD O28 P25 SING N N 19 A1EOD P25 O24 SING N N 20 A1EOD P25 O26 SING N N 21 A1EOD N08 C07 SING N N 22 A1EOD N08 C02 SING N N 23 A1EOD O01 C02 DOUB N N 24 A1EOD C07 C06 DOUB N N 25 A1EOD C02 N03 SING N N 26 A1EOD O30 C29 SING N N 27 A1EOD C06 C29 SING N N 28 A1EOD C06 C04 SING N N 29 A1EOD N03 C04 DOUB N N 30 A1EOD C04 N05 SING N N 31 A1EOD C10 H102 SING N N 32 A1EOD C10 H101 SING N N 33 A1EOD C13 H131 SING N N 34 A1EOD C15 H151 SING N N 35 A1EOD C15 H152 SING N N 36 A1EOD C07 H071 SING N N 37 A1EOD C09 H091 SING N N 38 A1EOD C11 H111 SING N N 39 A1EOD C29 H291 SING N N 40 A1EOD C29 H292 SING N N 41 A1EOD N05 H051 SING N N 42 A1EOD N05 H052 SING N N 43 A1EOD O12 H121 SING N N 44 A1EOD O19 H1 SING N N 45 A1EOD O23 H2 SING N N 46 A1EOD O26 H3 SING N N 47 A1EOD O28 H4 SING N N 48 A1EOD O30 H301 SING N N 49 # 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 A1EOD InChI InChI 1.06 "InChI=1S/C10H18N3O14P3/c11-9-5(3-14)2-13(10(16)12-9)8-1-6(15)7(25-8)4-24-29(20,21)27-30(22,23)26-28(17,18)19/h2,6-8,14-15H,1,3-4H2,(H,20,21)(H,22,23)(H2,11,12,16)(H2,17,18,19)/t6-,7+,8+/m0/s1" A1EOD InChIKey InChI 1.06 DLHNIFPAUZVLLA-XLPZGREQSA-N A1EOD SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1CO)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2" A1EOD SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1CO)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2" A1EOD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)CO)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" A1EOD SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(OC1N2C=C(C(=NC2=O)N)CO)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id A1EOD _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-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono 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 A1EOD "Create component" 2025-04-01 PDBC A1EOD "Initial release" 2026-02-11 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1EOD _pdbx_chem_comp_synonyms.name "2'-deoxy-5-hydroxymethyl-CTP" _pdbx_chem_comp_synonyms.provenance PUBCHEM _pdbx_chem_comp_synonyms.type ? #