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 
# 
