data_SUD # _chem_comp.id SUD _chem_comp.name "4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL 2-PHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H26 N3 O17 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-07-28 _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 601.287 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SUD _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 1U43 _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 SUD C1 C1 C 0 1 N N N 15.340 31.891 7.391 4.169 0.096 -0.520 C1 SUD 1 SUD N1 N1 N 0 1 N N N 8.304 30.677 12.872 -7.166 -0.455 -0.488 N1 SUD 2 SUD C3 C3 C 0 1 N N N 7.128 30.659 13.518 -6.808 -1.397 0.404 C3 SUD 3 SUD N3 N3 N 0 1 N N N 6.539 29.463 13.742 -7.468 -2.550 0.487 N3 SUD 4 SUD C4 C4 C 0 1 N N N 7.089 28.308 13.346 -8.492 -2.805 -0.317 C4 SUD 5 SUD C5 C5 C 0 1 N N N 8.373 28.334 12.649 -8.888 -1.841 -1.267 C5 SUD 6 SUD C6 C6 C 0 1 N N N 8.915 29.536 12.448 -8.211 -0.671 -1.336 C6 SUD 7 SUD O8 O8 O 0 1 N N N 6.588 31.683 13.897 -5.870 -1.186 1.155 O8 SUD 8 SUD N4 N4 N 0 1 N N N 6.443 27.184 13.602 -9.163 -4.002 -0.226 N4 SUD 9 SUD "C1'" C1* C 0 1 N N R 8.973 31.938 12.581 -6.424 0.807 -0.552 "C1'" SUD 10 SUD "C2'" C2* C 0 1 N N R 10.391 32.059 13.119 -6.514 1.566 0.797 "C2'" SUD 11 SUD "O2'" O2* O 0 1 N N N 10.443 33.210 13.960 -7.692 2.374 0.850 "O2'" SUD 12 SUD "C3'" C3* C 0 1 N N S 11.289 32.225 11.915 -5.240 2.449 0.758 "C3'" SUD 13 SUD "C4'" C4* C 0 1 N N R 10.327 32.395 10.726 -4.326 1.743 -0.262 "C4'" SUD 14 SUD "O4'" O4* O 0 1 N N N 9.031 32.027 11.175 -5.010 0.559 -0.705 "O4'" SUD 15 SUD "O3'" O3* O 0 1 N N N 12.094 33.392 12.014 -5.560 3.771 0.321 "O3'" SUD 16 SUD "C5'" C5* C 0 1 N N N 10.776 31.528 9.522 -3.002 1.360 0.403 "C5'" SUD 17 SUD "O5'" O5* O 0 1 N N N 11.261 30.192 9.833 -2.121 0.805 -0.576 "O5'" SUD 18 SUD PA PA P 0 1 N N R 11.798 29.171 8.682 -0.755 0.428 0.189 PA SUD 19 SUD O1A O1A O 0 1 N N N 10.953 27.812 8.619 -0.235 1.623 0.890 O1A SUD 20 SUD O2A O2A O 0 1 N N N 11.692 29.875 7.234 -1.045 -0.739 1.260 O2A SUD 21 SUD O3A O3A O 0 1 N N N 13.350 28.818 8.921 0.335 -0.084 -0.880 O3A SUD 22 SUD PB PB P 0 1 N N S 14.302 30.124 9.081 1.762 -0.060 -0.136 PB SUD 23 SUD O1B O1B O 0 1 N N N 13.878 30.945 10.405 1.859 1.151 0.709 O1B SUD 24 SUD O2B O2B O 0 1 N N N 14.213 31.139 7.845 2.939 -0.043 -1.235 O2B SUD 25 SUD O3B O3B O 0 1 N N N 15.818 29.616 9.281 1.908 -1.372 0.786 O3B SUD 26 SUD C27 C27 C 0 1 N N R 14.904 32.785 6.218 5.335 0.119 -1.511 C27 SUD 27 SUD C28 C28 C 0 1 N N S 16.044 33.087 5.203 6.657 0.143 -0.742 C28 SUD 28 SUD C29 C29 C 0 1 N N N 15.466 34.005 4.075 7.818 0.292 -1.728 C29 SUD 29 SUD O30 O30 O 0 1 N N N 16.494 34.337 3.123 7.805 -0.803 -2.647 O30 SUD 30 SUD O31 O31 O 0 1 N N N 16.556 31.819 4.642 6.806 -1.077 -0.012 O31 SUD 31 SUD C32 C32 C 0 1 N N N 17.260 33.799 5.852 6.660 1.323 0.231 C32 SUD 32 SUD O33 O33 O 0 1 N N N 14.421 34.031 6.748 5.240 1.286 -2.331 O33 SUD 33 SUD P34 P34 P 0 1 N N N 15.861 30.548 3.847 7.892 -0.798 1.143 P34 SUD 34 SUD O35 O35 O 0 1 N N N 15.223 30.977 2.582 9.111 -0.212 0.544 O35 SUD 35 SUD O36 O36 O 0 1 N N N 16.923 29.547 3.505 7.277 0.228 2.221 O36 SUD 36 SUD O37 O37 O 0 1 N N N 14.831 29.854 4.713 8.265 -2.184 1.874 O37 SUD 37 SUD H11 1H1 H 0 1 N N N 16.208 31.241 7.130 4.290 -0.745 0.163 H11 SUD 38 SUD H12 2H1 H 0 1 N N N 15.822 32.472 8.212 4.156 1.026 0.047 H12 SUD 39 SUD H5 H5 H 0 1 N N N 8.927 27.455 12.278 -9.719 -2.033 -1.929 H5 SUD 40 SUD H6 H6 H 0 1 N N N 9.884 29.587 11.923 -8.495 0.083 -2.055 H6 SUD 41 SUD HN41 1HN4 H 0 0 N N N 5.499 27.250 13.222 -9.911 -4.186 -0.815 HN41 SUD 42 SUD HN42 2HN4 H 0 0 N N N 6.862 26.304 13.300 -8.888 -4.664 0.429 HN42 SUD 43 SUD "H1'" H1* H 0 1 N N N 8.395 32.751 13.080 -6.796 1.428 -1.367 "H1'" SUD 44 SUD "H2'" H2* H 0 1 N N N 10.710 31.171 13.714 -6.483 0.872 1.636 "H2'" SUD 45 SUD H1 H1 H 0 1 N N N 11.328 33.286 14.296 -7.688 2.817 1.709 H1 SUD 46 SUD "H3'" H3* H 0 1 N N N 11.980 31.356 11.816 -4.765 2.478 1.739 "H3'" SUD 47 SUD "H4'" H4* H 0 1 N N N 10.325 33.452 10.371 -4.138 2.402 -1.110 "H4'" SUD 48 SUD H2 H2 H 0 1 N N N 12.659 33.496 11.257 -6.180 4.137 0.967 H2 SUD 49 SUD "H5'1" 1H5* H 0 0 N N N 11.543 32.078 8.928 -3.187 0.624 1.184 "H5'1" SUD 50 SUD "H5'2" 2H5* H 0 0 N N N 9.950 31.464 8.776 -2.546 2.248 0.841 "H5'2" SUD 51 SUD H2A H2A H 0 1 N N N 12.005 29.280 6.563 -1.381 -1.497 0.763 H2A SUD 52 SUD H3B H3B H 0 1 N N N 16.375 30.380 9.375 1.840 -2.136 0.198 H3B SUD 53 SUD H27 H27 H 0 1 N N N 14.114 32.228 5.662 5.295 -0.771 -2.139 H27 SUD 54 SUD H291 1H29 H 0 0 N N N 14.975 34.916 4.491 7.711 1.228 -2.276 H291 SUD 55 SUD H292 2H29 H 0 0 N N N 14.576 33.548 3.583 8.761 0.296 -1.181 H292 SUD 56 SUD H30 H30 H 0 1 N N N 16.143 34.894 2.438 8.551 -0.670 -3.249 H30 SUD 57 SUD H321 1H32 H 0 0 N N N 17.645 33.217 6.721 6.420 2.239 -0.308 H321 SUD 58 SUD H322 2H32 H 0 0 N N N 18.077 34.015 5.125 5.916 1.154 1.010 H322 SUD 59 SUD H323 3H32 H 0 0 N N N 16.942 34.727 6.381 7.647 1.417 0.686 H323 SUD 60 SUD H33 H33 H 0 1 N N N 14.152 34.583 6.023 5.278 2.048 -1.738 H33 SUD 61 SUD H36 H36 H 0 1 N N N 16.523 28.816 3.048 6.486 -0.191 2.587 H36 SUD 62 SUD H37 H37 H 0 1 N N N 14.431 29.123 4.256 8.916 -1.973 2.557 H37 SUD 63 # 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 SUD C1 O2B SING N N 1 SUD C1 C27 SING N N 2 SUD C1 H11 SING N N 3 SUD C1 H12 SING N N 4 SUD N1 C3 SING N N 5 SUD N1 C6 SING N N 6 SUD N1 "C1'" SING N N 7 SUD C3 N3 SING N N 8 SUD C3 O8 DOUB N N 9 SUD N3 C4 DOUB N N 10 SUD C4 C5 SING N N 11 SUD C4 N4 SING N N 12 SUD C5 C6 DOUB N N 13 SUD C5 H5 SING N N 14 SUD C6 H6 SING N N 15 SUD N4 HN41 SING N N 16 SUD N4 HN42 SING N N 17 SUD "C1'" "C2'" SING N N 18 SUD "C1'" "O4'" SING N N 19 SUD "C1'" "H1'" SING N N 20 SUD "C2'" "O2'" SING N N 21 SUD "C2'" "C3'" SING N N 22 SUD "C2'" "H2'" SING N N 23 SUD "O2'" H1 SING N N 24 SUD "C3'" "C4'" SING N N 25 SUD "C3'" "O3'" SING N N 26 SUD "C3'" "H3'" SING N N 27 SUD "C4'" "O4'" SING N N 28 SUD "C4'" "C5'" SING N N 29 SUD "C4'" "H4'" SING N N 30 SUD "O3'" H2 SING N N 31 SUD "C5'" "O5'" SING N N 32 SUD "C5'" "H5'1" SING N N 33 SUD "C5'" "H5'2" SING N N 34 SUD "O5'" PA SING N N 35 SUD PA O1A DOUB N N 36 SUD PA O2A SING N N 37 SUD PA O3A SING N N 38 SUD O2A H2A SING N N 39 SUD O3A PB SING N N 40 SUD PB O1B DOUB N N 41 SUD PB O2B SING N N 42 SUD PB O3B SING N N 43 SUD O3B H3B SING N N 44 SUD C27 C28 SING N N 45 SUD C27 O33 SING N N 46 SUD C27 H27 SING N N 47 SUD C28 C29 SING N N 48 SUD C28 O31 SING N N 49 SUD C28 C32 SING N N 50 SUD C29 O30 SING N N 51 SUD C29 H291 SING N N 52 SUD C29 H292 SING N N 53 SUD O30 H30 SING N N 54 SUD O31 P34 SING N N 55 SUD C32 H321 SING N N 56 SUD C32 H322 SING N N 57 SUD C32 H323 SING N N 58 SUD O33 H33 SING N N 59 SUD P34 O35 DOUB N N 60 SUD P34 O36 SING N N 61 SUD P34 O37 SING N N 62 SUD O36 H36 SING N N 63 SUD O37 H37 SING N N 64 # 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 SUD SMILES ACDLabs 10.04 "O=P(O)(O)OC(C)(CO)C(O)COP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O" SUD SMILES_CANONICAL CACTVS 3.341 "C[C@@](CO)(O[P](O)(O)=O)[C@H](O)CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N" SUD SMILES CACTVS 3.341 "C[C](CO)(O[P](O)(O)=O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N" SUD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@](CO)([C@@H](CO[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)O)OP(=O)(O)O" SUD SMILES "OpenEye OEToolkits" 1.5.0 "CC(CO)(C(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O)O)OP(=O)(O)O" SUD InChI InChI 1.03 "InChI=1S/C14H26N3O17P3/c1-14(6-18,33-35(23,24)25)8(19)5-31-37(28,29)34-36(26,27)30-4-7-10(20)11(21)12(32-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21H,4-6H2,1H3,(H,26,27)(H,28,29)(H2,15,16,22)(H2,23,24,25)/t7-,8-,10-,11-,12-,14+/m1/s1" SUD InChIKey InChI 1.03 HTJXTKBIUVFUAR-XHIBXCGHSA-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 SUD "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(R)-{[(S)-{[(2R,3S)-2,4-dihydroxy-3-methyl-3-(phosphonooxy)butyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine" SUD "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 [[(2R,3S)-2,4-dihydroxy-3-methyl-3-phosphonooxy-butoxy]-hydroxy-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 SUD "Create component" 2004-07-28 RCSB SUD "Modify descriptor" 2011-06-04 RCSB #