data_CDP # _chem_comp.id CDP _chem_comp.name "CYTIDINE-5'-DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H15 N3 O11 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-15 _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 403.176 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CDP _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 1GX1 _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 CDP O3B O3B O 0 1 N N N 0.185 16.288 82.535 -5.483 2.208 0.404 O3B CDP 1 CDP PB PB P 0 1 N N N 0.420 15.321 81.281 -5.253 0.897 -0.502 PB CDP 2 CDP O1B O1B O 0 1 N N N -0.116 14.080 81.799 -6.075 -0.216 0.023 O1B CDP 3 CDP O2B O2B O 0 1 N N N -0.288 16.007 80.031 -5.684 1.213 -2.021 O2B CDP 4 CDP O3A O3A O 0 1 N N N 2.024 15.123 81.262 -3.698 0.482 -0.461 O3A CDP 5 CDP PA PA P 0 1 N N R 3.024 13.896 81.329 -2.780 -0.313 0.596 PA CDP 6 CDP O1A O1A O 0 1 N N N 3.391 13.448 79.960 -3.496 -1.524 1.057 O1A CDP 7 CDP O2A O2A O 0 1 N N N 2.722 12.756 82.304 -2.466 0.638 1.856 O2A CDP 8 CDP "O5'" "O5'" O 0 1 N N N 4.269 14.707 81.891 -1.398 -0.743 -0.110 "O5'" CDP 9 CDP "C5'" "C5'" C 0 1 N N N 4.129 15.349 83.154 -0.414 -1.554 0.535 "C5'" CDP 10 CDP "C4'" "C4'" C 0 1 N N R 5.340 16.231 83.478 0.768 -1.770 -0.411 "C4'" CDP 11 CDP "O4'" "O4'" O 0 1 N N N 6.503 15.443 83.614 1.444 -0.523 -0.642 "O4'" CDP 12 CDP "C3'" "C3'" C 0 1 N N S 5.735 17.223 82.374 1.786 -2.731 0.234 "C3'" CDP 13 CDP "O3'" "O3'" O 0 1 N N N 4.947 18.426 82.364 1.956 -3.896 -0.575 "O3'" CDP 14 CDP "C2'" "C2'" C 0 1 N N R 7.206 17.489 82.632 3.099 -1.912 0.287 "C2'" CDP 15 CDP "O2'" "O2'" O 0 1 N N N 7.260 18.457 83.672 4.222 -2.725 -0.060 "O2'" CDP 16 CDP "C1'" "C1'" C 0 1 N N R 7.677 16.130 83.156 2.849 -0.826 -0.789 "C1'" CDP 17 CDP N1 N1 N 0 1 N N N 8.374 15.275 82.163 3.663 0.362 -0.523 N1 CDP 18 CDP C2 C2 C 0 1 N N N 9.725 15.035 82.419 3.505 1.038 0.630 C2 CDP 19 CDP O2 O2 O 0 1 N N N 10.320 15.690 83.280 2.681 0.652 1.443 O2 CDP 20 CDP N3 N3 N 0 1 N N N 10.412 14.046 81.777 4.232 2.121 0.898 N3 CDP 21 CDP C4 C4 C 0 1 N N N 9.825 13.340 80.762 5.134 2.562 0.031 C4 CDP 22 CDP N4 N4 N 0 1 N N N 10.573 12.448 80.117 5.880 3.681 0.319 N4 CDP 23 CDP C5 C5 C 0 1 N N N 8.443 13.572 80.496 5.325 1.877 -1.186 C5 CDP 24 CDP C6 C6 C 0 1 N N N 7.721 14.515 81.240 4.581 0.774 -1.442 C6 CDP 25 CDP "H5'1" "H5'1" H 0 0 N N N 3.228 15.980 83.132 -0.068 -1.054 1.440 "H5'1" CDP 26 CDP "H5'2" "H5'2" H 0 0 N N N 4.052 14.572 83.929 -0.852 -2.517 0.797 "H5'2" CDP 27 CDP "H4'" "H4'" H 0 1 N N N 5.023 16.763 84.387 0.415 -2.181 -1.357 "H4'" CDP 28 CDP "H3'" "H3'" H 0 1 N N N 5.548 16.808 81.373 1.466 -3.008 1.238 "H3'" CDP 29 CDP HA HA H 0 1 N N N 4.773 18.699 83.257 2.587 -4.536 -0.216 HA CDP 30 CDP "H2'" "H2'" H 0 1 N N N 7.796 17.851 81.777 3.237 -1.462 1.270 "H2'" CDP 31 CDP HB HB H 0 1 N N N 7.272 18.017 84.514 4.365 -3.474 0.535 HB CDP 32 CDP "H1'" "H1'" H 0 1 N N N 8.422 16.320 83.942 3.054 -1.218 -1.786 "H1'" CDP 33 CDP H4N1 H4N1 H 0 0 N N N 10.029 12.005 79.405 5.747 4.150 1.158 H4N1 CDP 34 CDP H4N2 H4N2 H 0 0 N N N 11.533 12.251 80.315 6.539 4.002 -0.317 H4N2 CDP 35 CDP H5 H5 H 0 1 N N N 7.948 13.016 79.714 6.055 2.224 -1.903 H5 CDP 36 CDP H6 H6 H 0 1 N N N 6.659 14.638 81.083 4.712 0.230 -2.365 H6 CDP 37 CDP HO1 HO1 H 0 1 N N N 2.659 11.938 81.826 -1.997 1.452 1.628 HO1 CDP 38 CDP HO2 HO2 H 0 1 N N N -1.208 16.144 80.223 -6.611 1.470 -2.121 HO2 CDP 39 CDP HO3 HO3 H 0 1 N N N 0.138 15.770 83.330 -4.974 2.979 0.117 HO3 CDP 40 # 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 CDP O3B PB SING N N 1 CDP PB O1B DOUB N N 2 CDP PB O2B SING N N 3 CDP PB O3A SING N N 4 CDP O3A PA SING N N 5 CDP PA O1A DOUB N N 6 CDP PA O2A SING N N 7 CDP PA "O5'" SING N N 8 CDP "O5'" "C5'" SING N N 9 CDP "C5'" "C4'" SING N N 10 CDP "C5'" "H5'1" SING N N 11 CDP "C5'" "H5'2" SING N N 12 CDP "C4'" "O4'" SING N N 13 CDP "C4'" "C3'" SING N N 14 CDP "C4'" "H4'" SING N N 15 CDP "O4'" "C1'" SING N N 16 CDP "C3'" "O3'" SING N N 17 CDP "C3'" "C2'" SING N N 18 CDP "C3'" "H3'" SING N N 19 CDP "O3'" HA SING N N 20 CDP "C2'" "O2'" SING N N 21 CDP "C2'" "C1'" SING N N 22 CDP "C2'" "H2'" SING N N 23 CDP "O2'" HB SING N N 24 CDP "C1'" N1 SING N N 25 CDP "C1'" "H1'" SING N N 26 CDP N1 C2 SING N N 27 CDP N1 C6 SING N N 28 CDP C2 O2 DOUB N N 29 CDP C2 N3 SING N N 30 CDP N3 C4 DOUB N N 31 CDP C4 N4 SING N N 32 CDP C4 C5 SING N N 33 CDP N4 H4N1 SING N N 34 CDP N4 H4N2 SING N N 35 CDP C5 C6 DOUB N N 36 CDP C5 H5 SING N N 37 CDP C6 H6 SING N N 38 CDP HO1 O2A SING N N 39 CDP HO2 O2B SING N N 40 CDP HO3 O3B SING N N 41 # 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 CDP SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O" CDP 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](O)[C@H]2O" CDP SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O" CDP 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)OP(=O)(O)O)O)O" CDP SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O" CDP InChI InChI 1.03 "InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" CDP InChIKey InChI 1.03 ZWIADYZPOWUWEW-XVFCMESISA-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 CDP "SYSTEMATIC NAME" ACDLabs 10.04 ;cytidine 5'-(trihydrogen diphosphate) ; CDP "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 phosphono 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 CDP "Create component" 1999-07-15 RCSB CDP "Modify descriptor" 2011-06-04 RCSB #