data_C5G # _chem_comp.id C5G _chem_comp.name ;[CYTIDINE-5'-PHOSPHATE]-BETA-GLUCOSYL-PHOSPHORIC ACID ESTER ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H25 N3 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-07-26 _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 565.317 _chem_comp.one_letter_code ? _chem_comp.three_letter_code C5G _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 1TZF _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 C5G N1 N1 N 0 1 Y N N 21.935 3.120 28.642 -5.978 0.775 0.705 N1 C5G 1 C5G C2 C2 C 0 1 Y N N 21.939 1.962 27.888 -5.765 1.504 -0.405 C2 C5G 2 C5G N3 N3 N 0 1 Y N N 22.254 0.834 28.594 -6.350 2.689 -0.573 N3 C5G 3 C5G C4 C4 C 0 1 Y N N 22.546 0.733 29.950 -7.161 3.181 0.355 C4 C5G 4 C5G C5 C5 C 0 1 Y N N 22.504 1.983 30.638 -7.400 2.444 1.533 C5 C5G 5 C5G C6 C6 C 0 1 Y N N 22.219 3.087 29.991 -6.802 1.239 1.686 C6 C5G 6 C5G O2 O2 O 0 1 N N N 21.674 1.905 26.685 -5.023 1.073 -1.273 O2 C5G 7 C5G N4 N4 N 0 1 N N N 22.796 -0.367 30.423 -7.759 4.406 0.171 N4 C5G 8 C5G C1D C1* C 0 1 N N R 21.595 4.395 27.998 -5.320 -0.524 0.861 C1D C5G 9 C5G C2D C2* C 0 1 N N R 20.393 5.057 28.652 -5.801 -1.505 -0.231 C2D C5G 10 C5G O2D O2* O 0 1 N N N 19.152 4.638 28.077 -6.820 -2.369 0.276 O2D C5G 11 C5G C3D C3* C 0 1 N N S 20.601 6.571 28.417 -4.533 -2.316 -0.591 C3D C5G 12 C5G C4D C4* C 0 1 N N R 22.116 6.637 28.307 -3.439 -1.730 0.330 C4D C5G 13 C5G O4D O4* O 0 1 N N N 22.650 5.288 28.134 -3.897 -0.397 0.645 O4D C5G 14 C5G O3D O3* O 0 1 N N N 19.933 7.090 27.271 -4.730 -3.704 -0.314 O3D C5G 15 C5G C5D C5* C 0 1 N N N 22.775 7.227 29.509 -2.098 -1.672 -0.403 C5D C5G 16 C5G O5D O5* O 0 1 N N N 22.488 6.364 30.620 -1.093 -1.169 0.480 O5D C5G 17 C5G PA PA P 0 1 N N R 22.440 6.985 32.106 0.284 -1.136 -0.353 PA C5G 18 C5G O1A O1A O 0 1 N N N 21.816 8.332 32.204 0.558 -2.481 -0.907 O1A C5G 19 C5G O2A O2A O 0 1 N N N 21.912 6.091 33.151 0.158 -0.075 -1.556 O2A C5G 20 C5G O3A O3A O 0 1 N N N 24.058 7.120 32.326 1.490 -0.702 0.622 O3A C5G 21 C5G PB PB P 0 1 N N R 24.808 8.069 33.279 2.860 -1.069 -0.140 PB C5G 22 C5G O1B O1B O 0 1 N N N 24.786 7.568 34.689 2.772 -0.631 -1.551 O1B C5G 23 C5G O2B O2B O 0 1 N N N 24.074 9.389 33.235 3.094 -2.660 -0.086 O2B C5G 24 C5G "O1'" "O1'" O 0 1 N N N 26.354 8.221 32.764 4.091 -0.320 0.578 "O1'" C5G 25 C5G "C1'" "C1'" C 0 1 N N R 26.602 8.340 31.375 5.253 -0.587 -0.209 "C1'" C5G 26 C5G "C2'" "C2'" C 0 1 N N R 28.076 8.015 31.264 6.488 -0.599 0.694 "C2'" C5G 27 C5G "O2'" "O2'" O 0 1 N N N 28.271 6.732 31.887 6.354 -1.632 1.673 "O2'" C5G 28 C5G "C3'" "C3'" C 0 1 N N S 28.907 9.085 32.004 6.609 0.757 1.395 "C3'" C5G 29 C5G "O3'" "O3'" O 0 1 N N N 30.318 8.892 31.856 7.836 0.816 2.125 "O3'" C5G 30 C5G "C4'" "C4'" C 0 1 N N S 28.574 10.452 31.461 6.591 1.861 0.331 "C4'" C5G 31 C5G "O4'" "O4'" O 0 1 N N N 29.374 11.480 32.040 6.554 3.140 0.966 "O4'" C5G 32 C5G "C5'" "C5'" C 0 1 N N R 27.060 10.715 31.605 5.349 1.688 -0.546 "C5'" C5G 33 C5G "C6'" "C6'" C 0 1 N N N 26.672 12.007 30.919 5.305 2.805 -1.590 "C6'" C5G 34 C5G "O6'" "O6'" O 0 1 N N N 25.276 12.257 31.103 4.085 2.719 -2.330 "O6'" C5G 35 C5G "O5'" "O5'" O 0 1 N N N 26.282 9.692 30.935 5.394 0.424 -1.205 "O5'" C5G 36 C5G H5 H5 H 0 1 N N N 22.708 2.019 31.698 -8.058 2.831 2.297 H5 C5G 37 C5G H6 H6 H 0 1 N N N 22.206 4.016 30.541 -6.974 0.654 2.577 H6 C5G 38 C5G H41 1H4 H 0 1 N N N 23.016 -0.563 31.379 -7.589 4.912 -0.639 H41 C5G 39 C5G H42 2H4 H 0 1 N N N 22.740 -1.035 29.681 -8.354 4.762 0.849 H42 C5G 40 C5G H1D H1* H 0 1 N N N 21.377 4.166 26.944 -5.518 -0.933 1.852 H1D C5G 41 C5G H2D H2* H 0 1 N N N 20.331 4.786 29.716 -6.164 -0.958 -1.101 H2D C5G 42 C5G "HO'2" 2HO* H 0 0 N N N 18.500 4.545 28.762 -7.034 -2.994 -0.430 "HO'2" C5G 43 C5G H3D H3* H 0 1 N N N 20.170 7.198 29.212 -4.269 -2.170 -1.638 H3D C5G 44 C5G H4D H4* H 0 1 N N N 22.331 7.286 27.445 -3.349 -2.325 1.238 H4D C5G 45 C5G H3T H3T H 0 1 N N N 19.011 7.206 27.467 -5.421 -4.013 -0.916 H3T C5G 46 C5G "H5'1" 1H5* H 0 0 N N N 22.399 8.243 29.699 -1.822 -2.673 -0.735 "H5'1" C5G 47 C5G "H5'2" 2H5* H 0 0 N N N 23.862 7.295 29.352 -2.184 -1.014 -1.268 "H5'2" C5G 48 C5G HO2A HO2A H 0 0 N N N 21.798 5.218 32.794 -0.020 0.786 -1.153 HO2A C5G 49 C5G HO2B HO2B H 0 0 N N N 23.920 9.696 34.121 3.146 -2.904 0.848 HO2B C5G 50 C5G "H1'" "H1'" H 0 1 N N N 25.994 7.680 30.739 5.148 -1.559 -0.692 "H1'" C5G 51 C5G "H2'" "H2'" H 0 1 N N N 28.396 7.997 30.212 7.379 -0.780 0.093 "H2'" C5G 52 C5G HOD "2HO'" H 0 1 N N N 28.314 6.058 31.219 6.281 -2.467 1.190 HOD C5G 53 C5G "H3'" "H3'" H 0 1 N N N 28.651 8.996 33.070 5.770 0.894 2.077 "H3'" C5G 54 C5G "HO'3" "3HO'" H 0 0 N N N 30.537 8.849 30.933 7.804 0.107 2.782 "HO'3" C5G 55 C5G "H4'" "H4'" H 0 1 N N N 28.822 10.471 30.389 7.486 1.786 -0.287 "H4'" C5G 56 C5G "HO'4" "4HO'" H 0 0 N N N 29.552 11.269 32.949 7.353 3.207 1.507 "HO'4" C5G 57 C5G "H5'" "H5'" H 0 1 N N N 26.859 10.739 32.686 4.456 1.740 0.077 "H5'" C5G 58 C5G "H6'1" "1H6'" H 0 0 N N N 26.886 11.924 29.843 5.360 3.772 -1.091 "H6'1" C5G 59 C5G "H6'2" "2H6'" H 0 0 N N N 27.250 12.837 31.352 6.151 2.699 -2.271 "H6'2" C5G 60 C5G "HO'6" "6HO'" H 0 0 N N N 25.083 12.312 32.032 4.098 3.439 -2.975 "HO'6" C5G 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 C5G N1 C2 SING Y N 1 C5G N1 C6 SING Y N 2 C5G N1 C1D SING N N 3 C5G C2 N3 SING Y N 4 C5G C2 O2 DOUB N N 5 C5G N3 C4 DOUB Y N 6 C5G C4 C5 SING Y N 7 C5G C4 N4 SING N N 8 C5G C5 C6 DOUB Y N 9 C5G C5 H5 SING N N 10 C5G C6 H6 SING N N 11 C5G N4 H41 SING N N 12 C5G N4 H42 SING N N 13 C5G C1D C2D SING N N 14 C5G C1D O4D SING N N 15 C5G C1D H1D SING N N 16 C5G C2D O2D SING N N 17 C5G C2D C3D SING N N 18 C5G C2D H2D SING N N 19 C5G O2D "HO'2" SING N N 20 C5G C3D C4D SING N N 21 C5G C3D O3D SING N N 22 C5G C3D H3D SING N N 23 C5G C4D O4D SING N N 24 C5G C4D C5D SING N N 25 C5G C4D H4D SING N N 26 C5G O3D H3T SING N N 27 C5G C5D O5D SING N N 28 C5G C5D "H5'1" SING N N 29 C5G C5D "H5'2" SING N N 30 C5G O5D PA SING N N 31 C5G PA O1A DOUB N N 32 C5G PA O2A SING N N 33 C5G PA O3A SING N N 34 C5G O2A HO2A SING N N 35 C5G O3A PB SING N N 36 C5G PB O1B DOUB N N 37 C5G PB O2B SING N N 38 C5G PB "O1'" SING N N 39 C5G O2B HO2B SING N N 40 C5G "O1'" "C1'" SING N N 41 C5G "C1'" "C2'" SING N N 42 C5G "C1'" "O5'" SING N N 43 C5G "C1'" "H1'" SING N N 44 C5G "C2'" "O2'" SING N N 45 C5G "C2'" "C3'" SING N N 46 C5G "C2'" "H2'" SING N N 47 C5G "O2'" HOD SING N N 48 C5G "C3'" "O3'" SING N N 49 C5G "C3'" "C4'" SING N N 50 C5G "C3'" "H3'" SING N N 51 C5G "O3'" "HO'3" SING N N 52 C5G "C4'" "O4'" SING N N 53 C5G "C4'" "C5'" SING N N 54 C5G "C4'" "H4'" SING N N 55 C5G "O4'" "HO'4" SING N N 56 C5G "C5'" "C6'" SING N N 57 C5G "C5'" "O5'" SING N N 58 C5G "C5'" "H5'" SING N N 59 C5G "C6'" "O6'" SING N N 60 C5G "C6'" "H6'1" SING N N 61 C5G "C6'" "H6'2" SING N N 62 C5G "O6'" "HO'6" 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 C5G SMILES ACDLabs 10.04 "O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=NC2=O)N)C(O)C3O" C5G SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H]2O" C5G SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)[CH](O)[CH]2O" C5G SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O" C5G SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O" C5G InChI InChI 1.03 "InChI=1S/C15H25N3O16P2/c16-7-1-2-18(15(25)17-7)13-11(23)9(21)6(31-13)4-30-35(26,27)34-36(28,29)33-14-12(24)10(22)8(20)5(3-19)32-14/h1-2,5-6,8-14,19-24H,3-4H2,(H,26,27)(H,28,29)(H2,16,17,25)/t5-,6-,8-,9-,10+,11-,12-,13-,14-/m1/s1" C5G InChIKey InChI 1.03 CGPHZDRCVSLMCF-JZMIEXBBSA-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 C5G "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" C5G "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]methyl [hydroxy-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-phosphoryl] 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 C5G "Create component" 2004-07-26 RCSB C5G "Modify descriptor" 2011-06-04 RCSB #