data_55T # _chem_comp.id 55T _chem_comp.name "5'-O-[(R)-[(S)-[3-(acetylamino)phenyl](phosphono)methoxy](hydroxy)phosphoryl]cytidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H24 N4 O12 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-07-30 _chem_comp.pdbx_modified_date 2016-09-02 _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 550.350 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 55T _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 5CXY _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 55T N1 N1 N 0 1 N N N -5.153 23.625 -36.789 -5.782 0.023 -0.472 N1 55T 1 55T O11 O1 O 0 1 N N N -1.364 18.441 -31.125 1.732 -3.903 0.006 O11 55T 2 55T O12 O2 O 0 1 N N N -2.909 18.604 -33.194 3.033 -2.925 -1.923 O12 55T 3 55T C2 C1 C 0 1 N N N -4.865 24.335 -37.964 -5.668 -0.618 0.706 C2 55T 4 55T O2 O3 O 0 1 N N N -4.892 23.756 -39.021 -4.781 -0.297 1.480 O2 55T 5 55T N3 N2 N 0 1 N N N -4.590 25.652 -37.974 -6.506 -1.597 1.040 N3 55T 6 55T C4 C2 C 0 1 N N N -4.542 26.321 -36.774 -7.479 -1.966 0.216 C4 55T 7 55T N4 N3 N 0 1 N N N -4.244 27.650 -36.740 -8.339 -2.979 0.572 N4 55T 8 55T C5 C3 C 0 1 N N N -4.823 25.653 -35.576 -7.626 -1.314 -1.025 C5 55T 9 55T C6 C4 C 0 1 N N N -5.133 24.298 -35.626 -6.765 -0.320 -1.350 C6 55T 10 55T "C1'" C5 C 0 1 N N R -5.578 22.203 -36.936 -4.848 1.101 -0.808 "C1'" 55T 11 55T "O4'" O4 O 0 1 N N N -6.624 22.018 -35.959 -3.485 0.681 -0.586 "O4'" 55T 12 55T "C2'" C6 C 0 1 N N R -4.565 21.070 -36.771 -5.021 2.296 0.164 "C2'" 55T 13 55T "O2'" O5 O 0 1 N N N -4.826 20.039 -37.731 -6.049 3.179 -0.291 "O2'" 55T 14 55T "C3'" C7 C 0 1 N N S -4.814 20.644 -35.339 -3.634 2.979 0.089 "C3'" 55T 15 55T "O3'" O6 O 0 1 N N N -4.450 19.279 -35.104 -3.667 4.080 -0.821 "O3'" 55T 16 55T "C4'" C8 C 0 1 N N R -6.299 20.912 -35.154 -2.697 1.874 -0.436 "C4'" 55T 17 55T "C5'" C9 C 0 1 N N N -6.758 21.204 -33.744 -1.568 1.629 0.566 "C5'" 55T 18 55T "O5'" O7 O 0 1 N N N -5.979 22.262 -33.240 -0.650 0.676 0.027 "O5'" 55T 19 55T P P1 P 0 1 N N N -5.159 22.140 -31.864 0.664 0.181 0.815 P 55T 20 55T O3P O8 O 0 1 N N N -6.106 21.856 -30.756 0.224 -0.623 2.139 O3P 55T 21 55T O1P O9 O 0 1 N N N -4.197 20.891 -32.177 1.528 -0.787 -0.138 O1P 55T 22 55T O2P O10 O 0 1 N N N -4.321 23.408 -31.671 1.481 1.354 1.198 O2P 55T 23 55T C8 C10 C 0 1 N N S -3.167 20.481 -31.318 2.799 -1.319 0.240 C8 55T 24 55T P9 P2 P 0 1 N N N -2.735 18.748 -31.718 2.984 -2.998 -0.445 P9 55T 25 55T O10 O11 O 0 1 N N N -3.764 17.825 -31.069 4.347 -3.655 0.105 O10 55T 26 55T C13 C11 C 0 1 Y N N -1.953 21.319 -31.498 3.894 -0.433 -0.297 C13 55T 27 55T C14 C12 C 0 1 Y N N -1.560 21.708 -32.793 3.695 0.278 -1.467 C14 55T 28 55T C15 C13 C 0 1 Y N N -0.391 22.447 -32.941 4.696 1.092 -1.963 C15 55T 29 55T C16 C14 C 0 1 Y N N 0.379 22.790 -31.843 5.899 1.197 -1.292 C16 55T 30 55T C17 C15 C 0 1 Y N N 0.017 22.431 -30.533 6.102 0.484 -0.117 C17 55T 31 55T C18 C16 C 0 1 Y N N -1.183 21.678 -30.375 5.092 -0.329 0.381 C18 55T 32 55T N19 N4 N 0 1 N N N 0.818 22.935 -29.534 7.319 0.588 0.564 N19 55T 33 55T C34 C17 C 0 1 N N N 1.590 23.776 -27.346 9.369 1.827 1.182 C34 55T 34 55T C32 C18 C 0 1 N N N 0.572 23.052 -28.225 8.004 1.749 0.548 C32 55T 35 55T O33 O12 O 0 1 N N N -0.425 22.600 -27.703 7.522 2.730 0.023 O33 55T 36 55T H1 H1 H 0 1 N N N -0.769 18.183 -31.819 0.871 -3.528 -0.226 H1 55T 37 55T H2 H2 H 0 1 N N N -4.059 28.143 -37.590 -8.236 -3.425 1.427 H2 55T 38 55T H3 H3 H 0 1 N N N -4.210 28.133 -35.865 -9.049 -3.247 -0.032 H3 55T 39 55T H4 H4 H 0 1 N N N -4.800 26.179 -34.633 -8.412 -1.603 -1.707 H4 55T 40 55T H5 H5 H 0 1 N N N -5.363 23.775 -34.709 -6.858 0.195 -2.295 H5 55T 41 55T H6 H6 H 0 1 N N N -6.023 22.094 -37.936 -4.990 1.422 -1.840 H6 55T 42 55T H7 H7 H 0 1 N N N -3.543 21.464 -36.876 -5.229 1.948 1.176 H7 55T 43 55T H8 H8 H 0 1 N N N -4.194 19.338 -37.624 -6.195 3.942 0.285 H8 55T 44 55T H9 H9 H 0 1 N N N -4.248 21.306 -34.667 -3.317 3.310 1.078 H9 55T 45 55T H10 H10 H 0 1 N N N -3.872 19.230 -34.351 -4.286 4.780 -0.570 H10 55T 46 55T H11 H11 H 0 1 N N N -6.847 20.028 -35.512 -2.282 2.167 -1.401 H11 55T 47 55T H12 H12 H 0 1 N N N -7.819 21.493 -33.750 -1.046 2.566 0.761 H12 55T 48 55T H13 H13 H 0 1 N N N -6.624 20.311 -33.116 -1.985 1.246 1.497 H13 55T 49 55T H14 H14 H 0 1 N N N -6.029 22.531 -30.092 -0.250 -1.446 1.960 H14 55T 50 55T H15 H15 H 0 1 N N N -3.487 20.488 -30.266 2.867 -1.361 1.327 H15 55T 51 55T H16 H16 H 0 1 N N N -4.265 17.383 -31.745 5.145 -3.161 -0.130 H16 55T 52 55T H17 H17 H 0 1 N N N -2.154 21.438 -33.654 2.756 0.198 -1.993 H17 55T 53 55T H18 H18 H 0 1 N N N -0.079 22.758 -33.927 4.538 1.646 -2.876 H18 55T 54 55T H19 H19 H 0 1 N N N 1.288 23.352 -31.998 6.681 1.833 -1.680 H19 55T 55 55T H20 H20 H 0 1 N N N -1.504 21.381 -29.387 5.245 -0.881 1.296 H20 55T 56 55T H21 H21 H 0 1 N N N 1.715 23.262 -29.830 7.670 -0.176 1.049 H21 55T 57 55T H22 H22 H 0 1 N N N 1.240 23.777 -26.303 9.632 0.855 1.599 H22 55T 58 55T H23 H23 H 0 1 N N N 2.559 23.260 -27.407 10.104 2.111 0.429 H23 55T 59 55T H24 H24 H 0 1 N N N 1.704 24.813 -27.695 9.358 2.573 1.977 H24 55T 60 # 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 55T O2 C2 DOUB N N 1 55T N3 C2 SING N N 2 55T N3 C4 DOUB N N 3 55T C2 N1 SING N N 4 55T "O2'" "C2'" SING N N 5 55T "C1'" N1 SING N N 6 55T "C1'" "C2'" SING N N 7 55T "C1'" "O4'" SING N N 8 55T N1 C6 SING N N 9 55T C4 N4 SING N N 10 55T C4 C5 SING N N 11 55T "C2'" "C3'" SING N N 12 55T "O4'" "C4'" SING N N 13 55T C6 C5 DOUB N N 14 55T "C3'" "C4'" SING N N 15 55T "C3'" "O3'" SING N N 16 55T "C4'" "C5'" SING N N 17 55T "C5'" "O5'" SING N N 18 55T "O5'" P SING N N 19 55T O12 P9 DOUB N N 20 55T C15 C14 DOUB Y N 21 55T C15 C16 SING Y N 22 55T C14 C13 SING Y N 23 55T O1P P SING N N 24 55T O1P C8 SING N N 25 55T P O2P DOUB N N 26 55T P O3P SING N N 27 55T C16 C17 DOUB Y N 28 55T P9 C8 SING N N 29 55T P9 O11 SING N N 30 55T P9 O10 SING N N 31 55T C13 C8 SING N N 32 55T C13 C18 DOUB Y N 33 55T C17 C18 SING Y N 34 55T C17 N19 SING N N 35 55T N19 C32 SING N N 36 55T C32 O33 DOUB N N 37 55T C32 C34 SING N N 38 55T O11 H1 SING N N 39 55T N4 H2 SING N N 40 55T N4 H3 SING N N 41 55T C5 H4 SING N N 42 55T C6 H5 SING N N 43 55T "C1'" H6 SING N N 44 55T "C2'" H7 SING N N 45 55T "O2'" H8 SING N N 46 55T "C3'" H9 SING N N 47 55T "O3'" H10 SING N N 48 55T "C4'" H11 SING N N 49 55T "C5'" H12 SING N N 50 55T "C5'" H13 SING N N 51 55T O3P H14 SING N N 52 55T C8 H15 SING N N 53 55T O10 H16 SING N N 54 55T C14 H17 SING N N 55 55T C15 H18 SING N N 56 55T C16 H19 SING N N 57 55T C18 H20 SING N N 58 55T N19 H21 SING N N 59 55T C34 H22 SING N N 60 55T C34 H23 SING N N 61 55T C34 H24 SING N N 62 # 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 55T SMILES ACDLabs 12.01 "N1(C=CC(=NC1=O)N)C2C(C(C(O2)COP(=O)(O)OC(P(O)(=O)O)c3cc(ccc3)NC(C)=O)O)O" 55T InChI InChI 1.03 "InChI=1S/C18H24N4O12P2/c1-9(23)20-11-4-2-3-10(7-11)17(35(27,28)29)34-36(30,31)32-8-12-14(24)15(25)16(33-12)22-6-5-13(19)21-18(22)26/h2-7,12,14-17,24-25H,8H2,1H3,(H,20,23)(H,30,31)(H2,19,21,26)(H2,27,28,29)/t12-,14-,15-,16-,17+/m1/s1" 55T InChIKey InChI 1.03 DIZKZDHPUBLUSO-NHMWIVBRSA-N 55T SMILES_CANONICAL CACTVS 3.385 "CC(=O)Nc1cccc(c1)[C@@H](O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=NC3=O)N)[P](O)(O)=O" 55T SMILES CACTVS 3.385 "CC(=O)Nc1cccc(c1)[CH](O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=NC3=O)N)[P](O)(O)=O" 55T SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CC(=O)Nc1cccc(c1)[C@@H](OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O)P(=O)(O)O" 55T SMILES "OpenEye OEToolkits" 1.9.2 "CC(=O)Nc1cccc(c1)C(OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O)P(=O)(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 55T "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-[(S)-[3-(acetylamino)phenyl](phosphono)methoxy](hydroxy)phosphoryl]cytidine" 55T "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(S)-(3-acetamidophenyl)-[[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-methyl]phosphonic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 55T "Create component" 2015-07-30 RCSB 55T "Initial release" 2016-09-07 RCSB #