data_CDC # _chem_comp.id CDC _chem_comp.name "[2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H26 N4 O11 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-09-25 _chem_comp.pdbx_modified_date 2011-06-04 _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 488.324 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CDC _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1JYL _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 CDC N1 N1 N 0 1 N N N -12.683 33.979 0.605 5.094 -0.536 0.567 N1 CDC 1 CDC C2 C2 C 0 1 N N N -12.740 34.018 -0.792 4.718 -1.312 -0.467 C2 CDC 2 CDC N3 N3 N 0 1 N N N -13.532 34.867 -1.455 5.308 -2.484 -0.697 N3 CDC 3 CDC C4 C4 C 0 1 N N N -14.342 35.746 -0.774 6.276 -2.922 0.097 C4 CDC 4 CDC C5 C5 C 0 1 N N N -14.345 35.780 0.641 6.689 -2.136 1.192 C5 CDC 5 CDC C6 C6 C 0 1 N N N -13.493 34.868 1.284 6.084 -0.944 1.409 C6 CDC 6 CDC O2 O2 O 0 1 N N N -12.054 33.257 -1.531 3.831 -0.930 -1.212 O2 CDC 7 CDC N4 N4 N 0 1 N N N -15.126 36.561 -1.517 6.874 -4.137 -0.148 N4 CDC 8 CDC "C1'" C1* C 0 1 N N R -11.809 32.992 1.298 4.431 0.751 0.790 "C1'" CDC 9 CDC "C2'" C2* C 0 1 N N R -10.666 33.565 2.073 4.629 1.690 -0.427 "C2'" CDC 10 CDC "O2'" O2* O 0 1 N N N -9.646 33.953 1.186 5.856 2.414 -0.318 "O2'" CDC 11 CDC "C3'" C3* C 0 1 N N S -10.324 32.428 3.015 3.411 2.643 -0.303 "C3'" CDC 12 CDC "C4'" C4* C 0 1 N N R -11.615 31.599 3.116 2.410 1.860 0.568 "C4'" CDC 13 CDC "O4'" O4* O 0 1 N N N -12.530 32.293 2.268 2.998 0.580 0.855 "O4'" CDC 14 CDC "O3'" O3* O 0 1 N N N -9.326 31.514 2.538 3.794 3.863 0.336 "O3'" CDC 15 CDC "C5'" C5* C 0 1 N N N -11.920 31.687 4.584 1.096 1.670 -0.192 "C5'" CDC 16 CDC "O5'" O5* O 0 1 N N N -13.023 32.532 4.864 0.139 1.041 0.661 "O5'" CDC 17 CDC PA PA P 0 1 N N S -12.777 33.908 5.769 -1.212 0.873 -0.199 PA CDC 18 CDC O1A O1A O 0 1 N N N -12.757 35.131 4.840 -0.913 0.139 -1.449 O1A CDC 19 CDC O2A O2A O 0 1 N N N -11.402 33.637 6.443 -1.803 2.326 -0.558 O2A CDC 20 CDC O3A O3A O 0 1 N N N -13.953 34.131 6.859 -2.297 0.050 0.660 O3A CDC 21 CDC PB PB P 0 1 N N N -14.271 32.973 7.969 -3.370 -0.538 -0.386 PB CDC 22 CDC O1B O1B O 0 1 N N N -15.000 31.644 7.295 -4.730 -0.908 0.392 O1B CDC 23 CDC O2B O2B O -1 1 N N N -13.014 32.646 8.813 -3.668 0.523 -1.468 O2B CDC 24 CDC O3B O3B O 0 1 N N N -15.392 33.613 8.823 -2.797 -1.808 -1.053 O3B CDC 25 CDC C14 C14 C 0 1 N N N -15.432 30.767 8.291 -5.677 -1.310 -0.600 C14 CDC 26 CDC C15 C15 C 0 1 N N N -16.183 29.555 7.662 -6.999 -1.677 0.076 C15 CDC 27 CDC N11 N11 N 1 1 N N N -17.601 29.381 8.175 -7.609 -0.469 0.649 N11 CDC 28 CDC C16 C16 C 0 1 N N N -18.516 29.005 7.091 -7.755 0.549 -0.399 C16 CDC 29 CDC C17 C17 C 0 1 N N N -17.559 28.342 9.213 -6.749 0.051 1.721 C17 CDC 30 CDC C18 C18 C 0 1 N N N -18.148 30.622 8.774 -8.930 -0.801 1.198 C18 CDC 31 CDC H5 H5 H 0 1 N N N -14.967 36.468 1.194 7.476 -2.479 1.847 H5 CDC 32 CDC H6 H6 H 0 1 N N N -13.470 34.861 2.364 6.382 -0.324 2.242 H6 CDC 33 CDC H41 1H4 H 0 1 N N N -15.761 37.244 -1.155 7.582 -4.454 0.434 H41 CDC 34 CDC H42 2H4 H 0 1 N N N -14.969 36.371 -2.486 6.588 -4.675 -0.902 H42 CDC 35 CDC "H1'" H1* H 0 1 N N N -11.431 32.383 0.463 4.803 1.220 1.701 "H1'" CDC 36 CDC "H2'" H2* H 0 1 N N N -10.866 34.486 2.640 4.592 1.129 -1.361 "H2'" CDC 37 CDC "HO'2" 2HO* H 0 0 N N N -10.004 34.040 0.310 5.919 2.977 -1.102 "HO'2" CDC 38 CDC "H3'" H3* H 0 1 N N N -9.937 32.873 3.944 2.984 2.846 -1.285 "H3'" CDC 39 CDC "H4'" H4* H 0 1 N N N -11.611 30.543 2.807 2.226 2.400 1.497 "H4'" CDC 40 CDC H3T H3T H 0 1 N N N -9.492 31.312 1.625 4.464 4.275 -0.226 H3T CDC 41 CDC "H5'1" 1H5* H 0 0 N N N -11.037 32.113 5.083 1.270 1.044 -1.067 "H5'1" CDC 42 CDC "H5'2" 2H5* H 0 0 N N N -12.154 30.677 4.951 0.717 2.642 -0.510 "H5'2" CDC 43 CDC HO2A HO2A H 0 0 N N N -10.727 33.582 5.776 -1.984 2.770 0.281 HO2A CDC 44 CDC H141 1H14 H 0 0 N N N -16.119 31.302 8.964 -5.292 -2.175 -1.140 H141 CDC 45 CDC H142 2H14 H 0 0 N N N -14.560 30.399 8.851 -5.842 -0.489 -1.298 H142 CDC 46 CDC H151 1H15 H 0 0 N N N -15.625 28.649 7.941 -6.813 -2.401 0.869 H151 CDC 47 CDC H152 2H15 H 0 0 N N N -16.230 29.710 6.574 -7.676 -2.111 -0.660 H152 CDC 48 CDC H161 1H16 H 0 0 N N N -18.200 28.043 6.662 -6.775 0.795 -0.807 H161 CDC 49 CDC H162 2H16 H 0 0 N N N -18.497 29.779 6.310 -8.393 0.163 -1.195 H162 CDC 50 CDC H163 3H16 H 0 0 N N N -19.537 28.911 7.489 -8.207 1.445 0.026 H163 CDC 51 CDC H171 1H17 H 0 0 N N N -18.447 28.431 9.857 -7.279 0.835 2.262 H171 CDC 52 CDC H172 2H17 H 0 0 N N N -16.651 28.468 9.821 -6.495 -0.756 2.407 H172 CDC 53 CDC H173 3H17 H 0 0 N N N -17.549 27.349 8.739 -5.837 0.461 1.288 H173 CDC 54 CDC H181 1H18 H 0 0 N N N -19.118 30.856 8.311 -9.568 -1.187 0.403 H181 CDC 55 CDC H182 2H18 H 0 0 N N N -17.448 31.453 8.599 -8.821 -1.557 1.976 H182 CDC 56 CDC H183 3H18 H 0 0 N N N -18.283 30.479 9.856 -9.382 0.095 1.623 H183 CDC 57 # 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 CDC N1 C2 SING N N 1 CDC N1 C6 SING N N 2 CDC N1 "C1'" SING N N 3 CDC C2 N3 SING N N 4 CDC C2 O2 DOUB N N 5 CDC N3 C4 DOUB N N 6 CDC C4 C5 SING N N 7 CDC C4 N4 SING N N 8 CDC C5 C6 DOUB N N 9 CDC C5 H5 SING N N 10 CDC C6 H6 SING N N 11 CDC N4 H41 SING N N 12 CDC N4 H42 SING N N 13 CDC "C1'" "C2'" SING N N 14 CDC "C1'" "O4'" SING N N 15 CDC "C1'" "H1'" SING N N 16 CDC "C2'" "O2'" SING N N 17 CDC "C2'" "C3'" SING N N 18 CDC "C2'" "H2'" SING N N 19 CDC "O2'" "HO'2" SING N N 20 CDC "C3'" "C4'" SING N N 21 CDC "C3'" "O3'" SING N N 22 CDC "C3'" "H3'" SING N N 23 CDC "C4'" "O4'" SING N N 24 CDC "C4'" "C5'" SING N N 25 CDC "C4'" "H4'" SING N N 26 CDC "O3'" H3T SING N N 27 CDC "C5'" "O5'" SING N N 28 CDC "C5'" "H5'1" SING N N 29 CDC "C5'" "H5'2" SING N N 30 CDC "O5'" PA SING N N 31 CDC PA O1A DOUB N N 32 CDC PA O2A SING N N 33 CDC PA O3A SING N N 34 CDC O2A HO2A SING N N 35 CDC O3A PB SING N N 36 CDC PB O1B SING N N 37 CDC PB O2B SING N N 38 CDC PB O3B DOUB N N 39 CDC O1B C14 SING N N 40 CDC C14 C15 SING N N 41 CDC C14 H141 SING N N 42 CDC C14 H142 SING N N 43 CDC C15 N11 SING N N 44 CDC C15 H151 SING N N 45 CDC C15 H152 SING N N 46 CDC N11 C16 SING N N 47 CDC N11 C17 SING N N 48 CDC N11 C18 SING N N 49 CDC C16 H161 SING N N 50 CDC C16 H162 SING N N 51 CDC C16 H163 SING N N 52 CDC C17 H171 SING N N 53 CDC C17 H172 SING N N 54 CDC C17 H173 SING N N 55 CDC C18 H181 SING N N 56 CDC C18 H182 SING N N 57 CDC C18 H183 SING N N 58 # 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 CDC SMILES ACDLabs 10.04 "[O-]P(=O)(OCC[N+](C)(C)C)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O" CDC SMILES_CANONICAL CACTVS 3.341 "C[N+](C)(C)CCO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N" CDC SMILES CACTVS 3.341 "C[N+](C)(C)CCO[P]([O-])(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N" CDC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[N+](C)(C)CCO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)O" CDC SMILES "OpenEye OEToolkits" 1.5.0 "C[N+](C)(C)CCOP(=O)([O-])OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O" CDC InChI InChI 1.03 "InChI=1S/C14H26N4O11P2/c1-18(2,3)6-7-26-30(22,23)29-31(24,25)27-8-9-11(19)12(20)13(28-9)17-5-4-10(15)16-14(17)21/h4-5,9,11-13,19-20H,6-8H2,1-3H3,(H3-,15,16,21,22,23,24,25)/t9-,11-,12-,13-/m1/s1" CDC InChIKey InChI 1.03 RZZPDXZPRHQOCG-OJAKKHQRSA-N # 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 CDC "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(S)-hydroxy({[2-(trimethylammonio)ethoxy]phosphinato}oxy)phosphoryl]cytidine" CDC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] 2-trimethylazaniumylethyl 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 CDC "Create component" 2001-09-25 RCSB CDC "Modify descriptor" 2011-06-04 RCSB #