data_1AA # _chem_comp.id 1AA _chem_comp.name "5'-O-[({[(2-{[(2-AMINOPHENYL)CARBONYL]OXY}ETHYL)OXY]PHOSPHINATO}OXY)PHOSPHINATO]CYTIDINE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H24 N4 O13 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-09-26 _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 566.350 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 1AA _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 2AMT _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 1AA O1 O1 O 0 1 N N N 4.729 4.867 15.141 -5.614 0.917 -1.262 O1 1AA 1 1AA C1 C1 C 0 1 N N N 3.763 5.623 15.072 -6.164 1.656 -0.463 C1 1AA 2 1AA N4 N4 N 0 1 N N N 3.447 6.423 16.180 -6.644 2.828 -0.877 N4 1AA 3 1AA "C9'" C9* C 0 1 N N N 2.352 7.294 16.136 -7.246 3.651 -0.028 "C9'" 1AA 4 1AA N3 N3 N 0 1 N N N 2.065 8.045 17.194 -7.737 4.858 -0.467 N3 1AA 5 1AA "C8'" C8* C 0 1 N N N 1.571 7.372 14.987 -7.375 3.283 1.327 "C8'" 1AA 6 1AA "C7'" C7* C 0 1 N N N 1.877 6.585 13.879 -6.887 2.086 1.731 "C7'" 1AA 7 1AA N2 N2 N 0 1 N N N 2.974 5.696 13.903 -6.276 1.274 0.823 N2 1AA 8 1AA C2 C2 C 0 1 N N R 3.304 4.851 12.709 -5.738 -0.020 1.248 C2 1AA 9 1AA "O2'" O2* O 0 1 N N N 3.230 5.655 11.492 -4.361 -0.153 0.834 "O2'" 1AA 10 1AA C3 C3 C 0 1 N N R 2.342 3.668 12.521 -6.481 -1.172 0.534 C3 1AA 11 1AA "O4'" O4* O 0 1 N N N 3.082 2.505 12.125 -7.492 -1.724 1.379 "O4'" 1AA 12 1AA C4 C4 C 0 1 N N S 1.427 4.128 11.393 -5.374 -2.216 0.259 C4 1AA 13 1AA "O3'" O3* O 0 1 N N N 0.955 3.007 10.636 -5.666 -3.445 0.928 "O3'" 1AA 14 1AA C5 C5 C 0 1 N N R 2.360 4.991 10.546 -4.096 -1.573 0.843 C5 1AA 15 1AA C6 C6 C 0 1 N N N 1.568 6.077 9.816 -2.886 -1.895 -0.036 C6 1AA 16 1AA O2 O2 O 0 1 N N N 0.866 6.925 10.744 -1.710 -1.327 0.547 O2 1AA 17 1AA P1 P1 P 0 1 N N S -0.393 7.812 10.277 -0.482 -1.703 -0.424 P1 1AA 18 1AA "O1'" O1* O 0 1 N N N 0.125 9.036 9.626 -0.782 -1.243 -1.799 "O1'" 1AA 19 1AA O9 O9 O 0 1 N N N -1.339 7.928 11.405 -0.269 -3.298 -0.427 O9 1AA 20 1AA O3 O3 O 0 1 N N N -1.079 6.839 9.180 0.858 -0.983 0.103 O3 1AA 21 1AA P2 P2 P 0 1 N N R -1.691 7.339 7.766 1.883 -0.941 -1.138 P2 1AA 22 1AA O8 O8 O 0 1 N N N -1.174 8.679 7.400 1.165 -0.506 -2.357 O8 1AA 23 1AA O7 O7 O 0 1 N N N -3.156 7.110 7.788 2.499 -2.410 -1.374 O7 1AA 24 1AA O4 O4 O 0 1 N N N -1.031 6.280 6.737 3.073 0.095 -0.818 O4 1AA 25 1AA C7 C7 C 0 1 N N N -1.240 4.868 6.875 3.878 0.176 -1.995 C7 1AA 26 1AA C8 C8 C 0 1 N N N 0.090 4.118 6.773 5.034 1.149 -1.756 C8 1AA 27 1AA O5 O5 O 0 1 N N N 0.259 3.559 5.449 5.910 0.618 -0.727 O5 1AA 28 1AA C9 C9 C 0 1 N N N 1.338 4.069 4.778 7.002 1.311 -0.348 C9 1AA 29 1AA O6 O6 O 0 1 N N N 2.252 4.622 5.393 7.254 2.380 -0.869 O6 1AA 30 1AA "C1'" C1* C 0 1 Y N N 1.402 3.938 3.245 7.891 0.772 0.696 "C1'" 1AA 31 1AA "C2'" C2* C 0 1 Y N N 0.223 3.746 2.522 7.542 -0.394 1.383 "C2'" 1AA 32 1AA "C3'" C3* C 0 1 Y N N 0.267 3.627 1.132 8.377 -0.892 2.358 "C3'" 1AA 33 1AA "C4'" C4* C 0 1 Y N N 1.485 3.696 0.457 9.563 -0.244 2.663 "C4'" 1AA 34 1AA "C5'" C5* C 0 1 Y N N 2.664 3.887 1.175 9.922 0.908 1.994 "C5'" 1AA 35 1AA "C6'" C6* C 0 1 Y N N 2.624 4.008 2.564 9.096 1.424 1.003 "C6'" 1AA 36 1AA N1 N1 N 0 1 N N N 3.765 4.191 3.224 9.455 2.583 0.328 N1 1AA 37 1AA HN31 1HN3 H 0 0 N N N 1.307 8.695 17.258 -7.644 5.110 -1.399 HN31 1AA 38 1AA HN32 2HN3 H 0 0 N N N 2.730 7.855 17.916 -8.181 5.456 0.155 HN32 1AA 39 1AA "H8'" H8* H 0 1 N N N 0.726 8.044 14.954 -7.863 3.941 2.030 "H8'" 1AA 40 1AA "H7'" H7* H 0 1 N N N 1.267 6.656 12.990 -6.977 1.780 2.763 "H7'" 1AA 41 1AA H2 H2 H 0 1 N N N 4.317 4.462 12.889 -5.822 -0.128 2.329 H2 1AA 42 1AA H3 H3 H 0 1 N N N 1.789 3.401 13.434 -6.916 -0.821 -0.402 H3 1AA 43 1AA "H4'" H4* H 0 1 N N N 3.246 2.536 11.190 -7.875 -2.473 0.902 "H4'" 1AA 44 1AA H4 H4 H 0 1 N N N 0.528 4.657 11.742 -5.262 -2.383 -0.812 H4 1AA 45 1AA H6 H6 H 0 1 N N N 0.851 3.260 9.726 -6.470 -3.799 0.523 H6 1AA 46 1AA H5 H5 H 0 1 N N N 2.894 4.379 9.805 -3.928 -1.921 1.862 H5 1AA 47 1AA H61 1H6 H 0 1 N N N 0.830 5.590 9.162 -2.768 -2.976 -0.111 H61 1AA 48 1AA H62 2H6 H 0 1 N N N 2.266 6.693 9.229 -3.037 -1.476 -1.030 H62 1AA 49 1AA HO9 HO9 H 0 1 N N N -0.856 7.953 12.223 -0.076 -3.556 0.485 HO9 1AA 50 1AA HO7 HO7 H 0 1 N N N -3.456 7.061 8.688 2.957 -2.655 -0.559 HO7 1AA 51 1AA H71 1H7 H 0 1 N N N -1.905 4.525 6.069 4.278 -0.811 -2.230 H71 1AA 52 1AA H72 2H7 H 0 1 N N N -1.694 4.665 7.856 3.271 0.530 -2.828 H72 1AA 53 1AA H81 1H8 H 0 1 N N N 0.093 3.299 7.507 5.597 1.279 -2.680 H81 1AA 54 1AA H82 2H8 H 0 1 N N N 0.914 4.818 6.976 4.637 2.112 -1.434 H82 1AA 55 1AA "H2'" H2* H 0 1 N N N -0.724 3.690 3.039 6.618 -0.903 1.150 "H2'" 1AA 56 1AA "H3'" H3* H 0 1 N N N -0.647 3.481 0.576 8.106 -1.794 2.888 "H3'" 1AA 57 1AA H1 H1 H 0 1 N N N 1.515 3.602 -0.618 10.211 -0.642 3.430 H1 1AA 58 1AA "H5'" H5* H 0 1 N N N 3.609 3.941 0.656 10.848 1.408 2.238 "H5'" 1AA 59 1AA HN11 1HN1 H 0 0 N N N 3.717 5.046 3.741 10.319 2.991 0.492 HN11 1AA 60 1AA HN12 2HN1 H 0 0 N N N 4.523 4.237 2.574 8.841 2.984 -0.307 HN12 1AA 61 # 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 1AA O1 C1 DOUB N N 1 1AA C1 N4 SING N N 2 1AA C1 N2 SING N N 3 1AA N4 "C9'" DOUB N N 4 1AA "C9'" N3 SING N N 5 1AA "C9'" "C8'" SING N N 6 1AA N3 HN31 SING N N 7 1AA N3 HN32 SING N N 8 1AA "C8'" "C7'" DOUB N N 9 1AA "C8'" "H8'" SING N N 10 1AA "C7'" N2 SING N N 11 1AA "C7'" "H7'" SING N N 12 1AA N2 C2 SING N N 13 1AA C2 "O2'" SING N N 14 1AA C2 C3 SING N N 15 1AA C2 H2 SING N N 16 1AA "O2'" C5 SING N N 17 1AA C3 "O4'" SING N N 18 1AA C3 C4 SING N N 19 1AA C3 H3 SING N N 20 1AA "O4'" "H4'" SING N N 21 1AA C4 "O3'" SING N N 22 1AA C4 C5 SING N N 23 1AA C4 H4 SING N N 24 1AA "O3'" H6 SING N N 25 1AA C5 C6 SING N N 26 1AA C5 H5 SING N N 27 1AA C6 O2 SING N N 28 1AA C6 H61 SING N N 29 1AA C6 H62 SING N N 30 1AA O2 P1 SING N N 31 1AA P1 "O1'" DOUB N N 32 1AA P1 O9 SING N N 33 1AA P1 O3 SING N N 34 1AA O9 HO9 SING N N 35 1AA O3 P2 SING N N 36 1AA P2 O8 DOUB N N 37 1AA P2 O7 SING N N 38 1AA P2 O4 SING N N 39 1AA O7 HO7 SING N N 40 1AA O4 C7 SING N N 41 1AA C7 C8 SING N N 42 1AA C7 H71 SING N N 43 1AA C7 H72 SING N N 44 1AA C8 O5 SING N N 45 1AA C8 H81 SING N N 46 1AA C8 H82 SING N N 47 1AA O5 C9 SING N N 48 1AA C9 O6 DOUB N N 49 1AA C9 "C1'" SING N N 50 1AA "C1'" "C2'" DOUB Y N 51 1AA "C1'" "C6'" SING Y N 52 1AA "C2'" "C3'" SING Y N 53 1AA "C2'" "H2'" SING N N 54 1AA "C3'" "C4'" DOUB Y N 55 1AA "C3'" "H3'" SING N N 56 1AA "C4'" "C5'" SING Y N 57 1AA "C4'" H1 SING N N 58 1AA "C5'" "C6'" DOUB Y N 59 1AA "C5'" "H5'" SING N N 60 1AA "C6'" N1 SING N N 61 1AA N1 HN11 SING N N 62 1AA N1 HN12 SING N N 63 # 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 1AA SMILES ACDLabs 10.04 "O=P(O)(OCCOC(=O)c1ccccc1N)OP(=O)(O)OCC3OC(N2C(=O)N=C(N)C=C2)C(O)C3O" 1AA SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OCCOC(=O)c3ccccc3N)[C@@H](O)[C@H]2O" 1AA SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OCCOC(=O)c3ccccc3N)[CH](O)[CH]2O" 1AA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc(c(c1)C(=O)OCCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O)N" 1AA SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc(c(c1)C(=O)OCCOP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O)N" 1AA InChI InChI 1.03 "InChI=1S/C18H24N4O13P2/c19-11-4-2-1-3-10(11)17(25)31-7-8-32-36(27,28)35-37(29,30)33-9-12-14(23)15(24)16(34-12)22-6-5-13(20)21-18(22)26/h1-6,12,14-16,23-24H,7-9,19H2,(H,27,28)(H,29,30)(H2,20,21,26)/t12-,14-,15-,16-/m1/s1" 1AA InChIKey InChI 1.03 PGXVRIOOHRVKLC-DTZQCDIJSA-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 1AA "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(S)-{[(R)-(2-{[(2-aminophenyl)carbonyl]oxy}ethoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine" 1AA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxyethyl 2-aminobenzoate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 1AA "Create component" 2005-09-26 RCSB 1AA "Modify descriptor" 2011-06-04 RCSB #